Starting phenix.real_space_refine on Thu Mar 5 16:39:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rn2_54078/03_2026/9rn2_54078.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rn2_54078/03_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_54078/03_2026/9rn2_54078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rn2_54078/03_2026/9rn2_54078.map" model { file = "/net/cci-nas-00/data/ceres_data/9rn2_54078/03_2026/9rn2_54078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rn2_54078/03_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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23353 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 2352 Classifications: {'peptide': 469} Incomplete info: {'truncation_to_alanine': 413} Link IDs: {'PTRANS': 11, 'TRANS': 457} Chain breaks: 10 Unresolved non-hydrogen bonds: 1626 Unresolved non-hydrogen angles: 2064 Unresolved non-hydrogen dihedrals: 1368 Unresolved non-hydrogen chiralities: 140 Planarities with less than four sites: {'ARG:plan': 39, 'GLU:plan': 26, 'ASN:plan1': 20, 'PHE:plan': 20, 'GLN:plan1': 28, 'ASP:plan': 19, 'TYR:plan': 19, 'HIS:plan': 17, 'TRP:plan': 7} Unresolved non-hydrogen planarities: 929 Chain: "J" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1677 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Unresolved non-hydrogen bonds: 980 Unresolved non-hydrogen angles: 1263 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'PHE:plan': 15, 'ASP:plan': 18, 'TYR:plan': 12, 'ARG:plan': 15, 'GLU:plan': 18, 'ASN:plan1': 14, 'TRP:plan': 5, 'GLN:plan1': 15, 'HIS:plan': 8} Unresolved non-hydrogen planarities: 562 Chain: "K" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1600 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Unresolved non-hydrogen bonds: 922 Unresolved non-hydrogen angles: 1182 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'ASP:plan': 21, 'ASN:plan1': 8, 'PHE:plan': 12, 'ARG:plan': 14, 'TRP:plan': 4, 'GLU:plan': 23, 'HIS:plan': 7, 'TYR:plan': 13, 'GLN:plan1': 9} Unresolved non-hydrogen planarities: 519 Chain: "L" Number of atoms: 1991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 1991 Classifications: {'peptide': 396} Incomplete info: {'truncation_to_alanine': 338} Link IDs: {'PTRANS': 16, 'TRANS': 379} Chain breaks: 5 Unresolved non-hydrogen bonds: 1157 Unresolved non-hydrogen angles: 1482 Unresolved non-hydrogen dihedrals: 934 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'ASP:plan': 27, 'GLU:plan': 23, 'TRP:plan': 6, 'ARG:plan': 19, 'ASN:plan1': 15, 'TYR:plan': 6, 'PHE:plan': 15, 'GLN:plan1': 16, 'HIS:plan': 6} Unresolved non-hydrogen planarities: 593 Chain: "M" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 1488 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 920 Unresolved non-hydrogen angles: 1174 Unresolved non-hydrogen dihedrals: 755 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'PHE:plan': 11, 'GLN:plan1': 13, 'GLU:plan': 27, 'ASP:plan': 21, 'TYR:plan': 8, 'ASN:plan1': 12, 'ARG:plan': 18, 'TRP:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 536 Chain: "N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 510 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 350 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 298 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 4, 'ASN:plan1': 8, 'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 7, 'TRP:plan': 2, 'PHE:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 232 Chain: "O" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 895 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 13, 'TRANS': 161} Chain breaks: 1 Unresolved non-hydrogen bonds: 573 Unresolved non-hydrogen angles: 744 Unresolved non-hydrogen dihedrals: 485 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'HIS:plan': 7, 'TYR:plan': 9, 'TRP:plan': 4, 'PHE:plan': 7, 'ASP:plan': 9, 'ASN:plan1': 8, 'GLU:plan': 14, 'ARG:plan': 11, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 362 Chain: "P" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 189 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 5, 'PHE:plan': 3, 'TYR:plan': 3, 'GLN:plan1': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 125 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 351 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 3, 'TRANS': 66} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 8, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 167 Chain: "V" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 275 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 63} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 283 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'PHE:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "W" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 373 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 5, 'TRANS': 67} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 3, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "X" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2803 Classifications: {'DNA': 138} Link IDs: {'rna3p': 137} Chain: "Y" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2855 Classifications: {'DNA': 138} Link IDs: {'rna3p': 137} Time building chain proxies: 5.57, per 1000 atoms: 0.24 Number of scatterers: 23353 At special positions: 0 Unit cell: (174.07, 172.38, 194.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 276 15.00 O 5050 8.00 N 4523 7.00 C 13490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 859.3 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: 2.99 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: 6.53 Time building geometry restraints manager: 2.62 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=" O5' DA X 131 " pdb=" C5' DA X 131 " ideal model delta sigma weight residual 1.423 1.328 0.095 3.00e-02 1.11e+03 1.01e+01 bond pdb=" C3' DA Y 91 " pdb=" O3' DA Y 91 " ideal model delta sigma weight residual 1.422 1.327 0.095 3.00e-02 1.11e+03 9.92e+00 bond pdb=" N GLY G 9 " pdb=" CA GLY G 9 " ideal model delta sigma weight residual 1.451 1.499 -0.048 1.60e-02 3.91e+03 9.07e+00 bond pdb=" N GLY J 12 " pdb=" CA GLY J 12 " ideal model delta sigma weight residual 1.451 1.498 -0.047 1.60e-02 3.91e+03 8.57e+00 bond pdb=" N GLY C 9 " pdb=" CA GLY C 9 " ideal model delta sigma weight residual 1.451 1.494 -0.043 1.60e-02 3.91e+03 7.08e+00 ... (remaining 24178 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 31706 2.07 - 4.14: 2190 4.14 - 6.20: 384 6.20 - 8.27: 52 8.27 - 10.34: 5 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 110.80 119.69 -8.89 1.50e+00 4.44e-01 3.51e+01 angle pdb=" N ASP N 415 " pdb=" CA ASP N 415 " pdb=" C ASP N 415 " ideal model delta sigma weight residual 108.55 117.95 -9.40 1.62e+00 3.81e-01 3.37e+01 angle pdb=" O3' DA Y 91 " pdb=" P DA Y 92 " pdb=" O5' DA Y 92 " ideal model delta sigma weight residual 104.00 95.43 8.57 1.50e+00 4.44e-01 3.26e+01 angle pdb=" C4' DA Y 60 " pdb=" C3' DA Y 60 " pdb=" O3' DA Y 60 " ideal model delta sigma weight residual 110.00 101.82 8.18 1.50e+00 4.44e-01 2.97e+01 angle pdb=" O3' DT X 68 " pdb=" P DA X 69 " pdb=" O5' DA X 69 " ideal model delta sigma weight residual 104.00 96.05 7.95 1.50e+00 4.44e-01 2.81e+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: 3345 0.085 - 0.169: 757 0.169 - 0.254: 93 0.254 - 0.338: 8 0.338 - 0.423: 1 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 -2.66 -2.36 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASP I 881 " pdb=" N ASP I 881 " pdb=" C ASP I 881 " pdb=" CB ASP I 881 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.550 Find NCS groups from input model: 0.160 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4445 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 0.095 24183 Z= 0.436 Angle : 1.156 10.339 34337 Z= 0.716 Chirality : 0.070 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 covalent geometry : bond 0.00855 (24183) covalent geometry : angle 1.15556 (34337) hydrogen bonds : bond 0.14747 ( 1733) hydrogen bonds : angle 5.77078 ( 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 : 0.656 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: 0.1387 time to fit residues: 66.3215 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 : 0.473 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 126 GLN C 39 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS E 69 GLN F 94 GLN H 83 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.118712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.079596 restraints weight = 100684.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.081459 restraints weight = 56385.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.082628 restraints weight = 38078.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.083633 restraints weight = 28912.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.084354 restraints weight = 23558.488| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.159 24183 Z= 0.516 Angle : 0.925 14.917 34337 Z= 0.521 Chirality : 0.051 0.281 4204 Planarity : 0.007 0.073 3714 Dihedral : 25.985 88.955 6163 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.14 % Allowed : 4.13 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3004 helix: 0.65 (0.12), residues: 1800 sheet: -0.50 (0.41), residues: 165 loop : -0.52 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 87 TYR 0.022 0.003 TYR F 89 PHE 0.025 0.002 PHE F 101 TRP 0.000 0.000 TRP I 764 HIS 0.012 0.003 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.01072 (24183) covalent geometry : angle 0.92500 (34337) hydrogen bonds : bond 0.10881 ( 1733) hydrogen bonds : angle 4.99890 ( 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 190 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.9519 (mtm) cc_final: 0.9222 (mtp) REVERT: A 106 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8569 (tm-30) REVERT: B 69 ASP cc_start: 0.9528 (m-30) cc_final: 0.9261 (m-30) REVERT: C 57 GLU cc_start: 0.9146 (tt0) cc_final: 0.8621 (mt-10) REVERT: C 65 GLU cc_start: 0.9643 (tt0) cc_final: 0.9149 (tp30) REVERT: D 63 MET cc_start: 0.9648 (mmm) cc_final: 0.9435 (mmm) REVERT: D 70 ILE cc_start: 0.9667 (mm) cc_final: 0.9458 (mm) REVERT: E 51 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8550 (mt-10) REVERT: F 64 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9145 (mt-10) REVERT: F 69 ASP cc_start: 0.9235 (m-30) cc_final: 0.9006 (t0) REVERT: H 66 PHE cc_start: 0.9530 (t80) cc_final: 0.9288 (t80) REVERT: H 114 GLU cc_start: 0.9410 (mm-30) cc_final: 0.9145 (mm-30) outliers start: 1 outliers final: 1 residues processed: 190 average time/residue: 0.1368 time to fit residues: 42.5869 Evaluate side-chains 158 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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: 7.9990 chunk 293 optimal weight: 4.9990 chunk 252 optimal weight: 50.0000 chunk 260 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 143 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.154990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.111743 restraints weight = 197169.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.110965 restraints weight = 97299.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.111187 restraints weight = 63490.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.110747 restraints weight = 53454.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.110598 restraints weight = 50289.635| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 24183 Z= 0.214 Angle : 0.612 11.870 34337 Z= 0.352 Chirality : 0.040 0.149 4204 Planarity : 0.005 0.072 3714 Dihedral : 25.639 89.411 6163 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.15), residues: 3004 helix: 1.69 (0.12), residues: 1787 sheet: -0.44 (0.41), residues: 176 loop : -0.34 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 117 TYR 0.014 0.002 TYR F 52 PHE 0.010 0.001 PHE E 68 TRP 0.000 0.000 TRP I 764 HIS 0.007 0.002 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00449 (24183) covalent geometry : angle 0.61216 (34337) hydrogen bonds : bond 0.04842 ( 1733) hydrogen bonds : angle 3.96839 ( 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 200 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.778 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: 0.9604 (mtm) cc_final: 0.9338 (mtp) REVERT: A 105 PHE cc_start: 0.9644 (m-80) cc_final: 0.9138 (m-10) REVERT: A 106 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 110 LEU cc_start: 0.9501 (mt) cc_final: 0.9299 (mt) REVERT: A 121 MET cc_start: 0.8649 (ptp) cc_final: 0.8337 (ptp) REVERT: B 69 ASP cc_start: 0.9391 (m-30) cc_final: 0.9035 (m-30) REVERT: B 94 GLN cc_start: 0.9293 (tm-30) cc_final: 0.8902 (tm-30) REVERT: C 57 GLU cc_start: 0.9013 (tt0) cc_final: 0.8524 (tt0) REVERT: C 65 GLU cc_start: 0.9572 (tt0) cc_final: 0.9037 (tp30) REVERT: D 63 MET cc_start: 0.9630 (mmm) cc_final: 0.9390 (mmm) REVERT: D 70 ILE cc_start: 0.9694 (mm) cc_final: 0.9484 (mm) REVERT: D 90 ILE cc_start: 0.9492 (tp) cc_final: 0.9156 (tp) REVERT: D 114 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8310 (tm-30) REVERT: E 51 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8376 (mt-10) REVERT: E 91 MET cc_start: 0.9464 (mmp) cc_final: 0.9186 (mmm) REVERT: E 95 GLU cc_start: 0.8843 (tp30) cc_final: 0.8541 (tp30) REVERT: E 101 LEU cc_start: 0.9805 (mt) cc_final: 0.9556 (mm) REVERT: E 104 LEU cc_start: 0.9616 (mm) cc_final: 0.9346 (mm) REVERT: E 105 PHE cc_start: 0.9598 (m-10) cc_final: 0.9263 (m-80) REVERT: F 61 VAL cc_start: 0.9743 (t) cc_final: 0.9180 (t) REVERT: F 64 GLU cc_start: 0.9357 (mt-10) cc_final: 0.8901 (mt-10) REVERT: F 69 ASP cc_start: 0.9050 (m-30) cc_final: 0.8842 (t0) REVERT: G 91 ASP cc_start: 0.8960 (t0) cc_final: 0.8420 (t0) REVERT: G 94 LEU cc_start: 0.9807 (mt) cc_final: 0.9499 (mt) REVERT: H 66 PHE cc_start: 0.9698 (t80) cc_final: 0.9465 (t80) REVERT: H 114 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9096 (mm-30) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.1287 time to fit residues: 43.1060 Evaluate side-chains 167 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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: 7.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 40.0000 chunk 186 optimal weight: 6.9990 chunk 122 optimal weight: 30.0000 chunk 316 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 320 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 293 optimal weight: 8.9990 chunk 235 optimal weight: 0.0770 overall best weight: 3.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.153914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.109158 restraints weight = 195645.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.108444 restraints weight = 99637.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.108417 restraints weight = 66008.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.107587 restraints weight = 55301.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.107493 restraints weight = 53609.894| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 24183 Z= 0.230 Angle : 0.593 13.282 34337 Z= 0.340 Chirality : 0.039 0.227 4204 Planarity : 0.004 0.047 3714 Dihedral : 25.296 87.464 6163 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: 1.49 (0.16), residues: 3004 helix: 1.94 (0.12), residues: 1785 sheet: -0.34 (0.42), residues: 169 loop : -0.39 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 73 TYR 0.017 0.001 TYR B 52 PHE 0.014 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00493 (24183) covalent geometry : angle 0.59340 (34337) hydrogen bonds : bond 0.05603 ( 1733) hydrogen bonds : angle 3.76482 ( 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 189 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.466 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: 0.9571 (mtm) cc_final: 0.9291 (mtp) REVERT: A 104 LEU cc_start: 0.9698 (mt) cc_final: 0.9495 (mt) REVERT: A 106 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8282 (tm-30) REVERT: A 110 LEU cc_start: 0.9355 (mt) cc_final: 0.8907 (mt) REVERT: A 130 ARG cc_start: 0.8781 (mmp80) cc_final: 0.8453 (mmp80) REVERT: B 69 ASP cc_start: 0.9297 (m-30) cc_final: 0.9030 (m-30) REVERT: C 65 GLU cc_start: 0.9329 (tt0) cc_final: 0.8965 (tp30) REVERT: C 115 VAL cc_start: 0.6360 (t) cc_final: 0.6016 (t) REVERT: D 63 MET cc_start: 0.9604 (mmm) cc_final: 0.9347 (mmm) REVERT: D 90 ILE cc_start: 0.9478 (tp) cc_final: 0.9247 (tp) REVERT: D 114 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8289 (tm-30) REVERT: E 51 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8401 (mt-10) REVERT: E 91 MET cc_start: 0.9431 (mmp) cc_final: 0.9139 (mmm) REVERT: E 95 GLU cc_start: 0.8856 (tp30) cc_final: 0.8389 (tt0) REVERT: E 101 LEU cc_start: 0.9811 (mt) cc_final: 0.9511 (mt) REVERT: E 104 LEU cc_start: 0.9611 (mm) cc_final: 0.9365 (mm) REVERT: E 105 PHE cc_start: 0.9473 (m-10) cc_final: 0.9083 (m-10) REVERT: F 64 GLU cc_start: 0.9332 (mt-10) cc_final: 0.8998 (mt-10) REVERT: G 91 ASP cc_start: 0.8907 (t0) cc_final: 0.8381 (t0) REVERT: G 94 LEU cc_start: 0.9813 (mt) cc_final: 0.9515 (mt) REVERT: H 66 PHE cc_start: 0.9692 (t80) cc_final: 0.9469 (t80) REVERT: H 101 LEU cc_start: 0.9720 (mt) cc_final: 0.9499 (mt) REVERT: H 114 GLU cc_start: 0.9325 (mm-30) cc_final: 0.9052 (mm-30) outliers start: 1 outliers final: 1 residues processed: 189 average time/residue: 0.1280 time to fit residues: 41.2076 Evaluate side-chains 164 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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: 4.9990 chunk 42 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 271 optimal weight: 40.0000 chunk 313 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.152689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.106114 restraints weight = 196336.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.105953 restraints weight = 90427.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.106494 restraints weight = 58992.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.106542 restraints weight = 42726.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.106376 restraints weight = 37377.590| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 24183 Z= 0.229 Angle : 0.602 13.381 34337 Z= 0.346 Chirality : 0.040 0.238 4204 Planarity : 0.005 0.044 3714 Dihedral : 25.277 86.256 6163 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.14 % Allowed : 3.44 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.43 (0.16), residues: 3004 helix: 1.90 (0.12), residues: 1800 sheet: -0.23 (0.43), residues: 168 loop : -0.52 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 93 TYR 0.025 0.002 TYR E 42 PHE 0.011 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.006 0.002 HIS F 76 Details of bonding type rmsd covalent geometry : bond 0.00479 (24183) covalent geometry : angle 0.60192 (34337) hydrogen bonds : bond 0.05322 ( 1733) hydrogen bonds : angle 3.76088 ( 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 190 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.622 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: 0.9568 (mtm) cc_final: 0.9294 (mtp) REVERT: A 106 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 110 LEU cc_start: 0.9303 (mt) cc_final: 0.8922 (mt) REVERT: C 65 GLU cc_start: 0.9105 (tt0) cc_final: 0.8770 (tp30) REVERT: C 113 GLN cc_start: 0.7297 (tp-100) cc_final: 0.7079 (tp-100) REVERT: C 115 VAL cc_start: 0.7374 (t) cc_final: 0.6915 (p) REVERT: D 34 ARG cc_start: 0.6890 (ptt-90) cc_final: 0.6600 (ptt180) REVERT: D 63 MET cc_start: 0.9657 (mmm) cc_final: 0.9445 (mmm) REVERT: D 114 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8250 (tm-30) REVERT: E 51 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8217 (mt-10) REVERT: E 91 MET cc_start: 0.9424 (mmp) cc_final: 0.9182 (mmm) REVERT: E 95 GLU cc_start: 0.8737 (tp30) cc_final: 0.8319 (tt0) REVERT: E 104 LEU cc_start: 0.9581 (mm) cc_final: 0.9353 (mm) REVERT: E 125 ILE cc_start: 0.9869 (tp) cc_final: 0.9509 (tp) REVERT: F 61 VAL cc_start: 0.9699 (t) cc_final: 0.9197 (t) REVERT: F 64 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8857 (mt-10) REVERT: F 69 ASP cc_start: 0.9052 (m-30) cc_final: 0.8788 (m-30) REVERT: G 113 GLN cc_start: 0.8126 (tp40) cc_final: 0.7726 (tp40) REVERT: H 66 PHE cc_start: 0.9718 (t80) cc_final: 0.9505 (t80) REVERT: H 101 LEU cc_start: 0.9741 (mt) cc_final: 0.9412 (mt) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1242 time to fit residues: 39.5028 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 : 0.569 ------------------------------------------------------------------------------- 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: 3.9990 chunk 227 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 242 optimal weight: 40.0000 chunk 55 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 169 optimal weight: 50.0000 chunk 196 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 118 optimal weight: 40.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.117258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.078387 restraints weight = 102804.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.080210 restraints weight = 58617.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.081346 restraints weight = 39914.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.082362 restraints weight = 30484.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.083021 restraints weight = 24757.643| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.5933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.150 24183 Z= 0.377 Angle : 0.725 18.714 34337 Z= 0.414 Chirality : 0.044 0.296 4204 Planarity : 0.005 0.065 3714 Dihedral : 25.474 89.970 6163 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 0.77 (0.15), residues: 3004 helix: 1.39 (0.12), residues: 1808 sheet: -0.40 (0.45), residues: 157 loop : -0.86 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 80 TYR 0.020 0.002 TYR F 89 PHE 0.014 0.002 PHE H 71 TRP 0.000 0.000 TRP I 764 HIS 0.009 0.002 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00800 (24183) covalent geometry : angle 0.72544 (34337) hydrogen bonds : bond 0.09060 ( 1733) hydrogen bonds : angle 4.34001 ( 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 166 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 110 LEU cc_start: 0.9234 (mt) cc_final: 0.8942 (mt) REVERT: A 121 MET cc_start: 0.8539 (ptp) cc_final: 0.8093 (mpp) REVERT: B 69 ASP cc_start: 0.9572 (m-30) cc_final: 0.9240 (m-30) REVERT: B 85 MET cc_start: 0.9399 (mmt) cc_final: 0.9164 (mmt) REVERT: C 65 GLU cc_start: 0.9169 (tt0) cc_final: 0.8826 (tp30) REVERT: C 113 GLN cc_start: 0.7400 (tp-100) cc_final: 0.7083 (tp-100) REVERT: C 115 VAL cc_start: 0.6723 (t) cc_final: 0.6237 (p) REVERT: D 34 ARG cc_start: 0.6609 (ptt-90) cc_final: 0.6328 (ptt180) REVERT: D 114 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8363 (tm-30) REVERT: E 95 GLU cc_start: 0.8846 (tp30) cc_final: 0.8462 (tt0) REVERT: F 64 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9050 (mt-10) REVERT: H 101 LEU cc_start: 0.9821 (mt) cc_final: 0.9553 (mt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1180 time to fit residues: 33.5859 Evaluate side-chains 138 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 2.9990 chunk 197 optimal weight: 20.0000 chunk 243 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 323 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS D 85 ASN E 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.153127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.107482 restraints weight = 198740.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.107383 restraints weight = 87986.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.107516 restraints weight = 57177.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.107798 restraints weight = 45857.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.108418 restraints weight = 42325.975| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 24183 Z= 0.153 Angle : 0.566 14.086 34337 Z= 0.323 Chirality : 0.039 0.152 4204 Planarity : 0.004 0.044 3714 Dihedral : 25.405 83.728 6163 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.14 % Allowed : 1.38 % Favored : 98.48 % 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: 1.46 (0.16), residues: 3004 helix: 1.99 (0.12), residues: 1812 sheet: 0.00 (0.46), residues: 155 loop : -0.71 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 87 TYR 0.016 0.001 TYR E 42 PHE 0.010 0.001 PHE C 26 TRP 0.000 0.000 TRP I 764 HIS 0.009 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00326 (24183) covalent geometry : angle 0.56577 (34337) hydrogen bonds : bond 0.03740 ( 1733) hydrogen bonds : angle 3.60140 ( 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 191 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.9566 (mtm) cc_final: 0.9285 (mtp) REVERT: A 106 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8547 (tm-30) REVERT: A 110 LEU cc_start: 0.9327 (mt) cc_final: 0.9013 (mt) REVERT: B 64 GLU cc_start: 0.8937 (mp0) cc_final: 0.8556 (mp0) REVERT: B 68 ARG cc_start: 0.9440 (ttp-110) cc_final: 0.8989 (ttm110) REVERT: B 69 ASP cc_start: 0.9365 (m-30) cc_final: 0.9074 (m-30) REVERT: B 85 MET cc_start: 0.9472 (mmt) cc_final: 0.9232 (mmt) REVERT: C 65 GLU cc_start: 0.9131 (tt0) cc_final: 0.8812 (tp30) REVERT: C 100 ARG cc_start: 0.8656 (mmp80) cc_final: 0.8401 (mmm160) REVERT: C 113 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7464 (tp-100) REVERT: C 115 VAL cc_start: 0.7942 (t) cc_final: 0.7511 (p) REVERT: D 34 ARG cc_start: 0.7033 (ptt-90) cc_final: 0.6652 (ptt180) REVERT: D 114 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8233 (tm-30) REVERT: E 51 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8083 (mt-10) REVERT: E 74 GLU cc_start: 0.9023 (tt0) cc_final: 0.8754 (tt0) REVERT: E 95 GLU cc_start: 0.8707 (tp30) cc_final: 0.8228 (tt0) REVERT: E 104 LEU cc_start: 0.9617 (mm) cc_final: 0.9412 (mm) REVERT: E 105 PHE cc_start: 0.9387 (m-10) cc_final: 0.8906 (m-10) REVERT: F 61 VAL cc_start: 0.9709 (t) cc_final: 0.9236 (t) REVERT: F 64 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8715 (mt-10) REVERT: F 71 VAL cc_start: 0.9815 (m) cc_final: 0.9395 (p) REVERT: F 85 MET cc_start: 0.9054 (tpt) cc_final: 0.8828 (tpp) REVERT: G 91 ASP cc_start: 0.8836 (t0) cc_final: 0.8479 (t0) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.1259 time to fit residues: 40.5573 Evaluate side-chains 156 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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: 40.0000 chunk 190 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 293 optimal weight: 0.0060 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 232 optimal weight: 30.0000 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.152799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.107561 restraints weight = 196695.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.106988 restraints weight = 92255.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.107665 restraints weight = 57308.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.107152 restraints weight = 44310.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.107306 restraints weight = 39086.393| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 24183 Z= 0.164 Angle : 0.550 13.843 34337 Z= 0.314 Chirality : 0.038 0.136 4204 Planarity : 0.004 0.043 3714 Dihedral : 25.120 83.431 6163 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: 1.64 (0.16), residues: 3004 helix: 2.13 (0.12), residues: 1810 sheet: 0.06 (0.46), residues: 155 loop : -0.64 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 18 TYR 0.015 0.001 TYR F 73 PHE 0.009 0.001 PHE E 68 TRP 0.000 0.000 TRP I 764 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00349 (24183) covalent geometry : angle 0.55042 (34337) hydrogen bonds : bond 0.04304 ( 1733) hydrogen bonds : angle 3.50853 ( 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 189 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8527 (pp) cc_final: 0.8285 (pp) REVERT: A 91 MET cc_start: 0.9580 (mtm) cc_final: 0.9264 (mtp) REVERT: A 106 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8507 (tm-30) REVERT: A 110 LEU cc_start: 0.9335 (mt) cc_final: 0.9017 (mt) REVERT: A 121 MET cc_start: 0.8737 (ptp) cc_final: 0.8179 (mpp) REVERT: B 64 GLU cc_start: 0.9062 (mp0) cc_final: 0.8785 (mm-30) REVERT: B 68 ARG cc_start: 0.9381 (ttp-110) cc_final: 0.9082 (ttm110) REVERT: B 69 ASP cc_start: 0.9293 (m-30) cc_final: 0.9051 (m-30) REVERT: B 85 MET cc_start: 0.9301 (mmt) cc_final: 0.9098 (mmt) REVERT: C 65 GLU cc_start: 0.9074 (tt0) cc_final: 0.8762 (tp30) REVERT: C 100 ARG cc_start: 0.8590 (mmp80) cc_final: 0.8287 (mmm160) REVERT: C 113 GLN cc_start: 0.7329 (tp-100) cc_final: 0.7074 (tp-100) REVERT: C 115 VAL cc_start: 0.7592 (t) cc_final: 0.7139 (p) REVERT: D 34 ARG cc_start: 0.7125 (ptt-90) cc_final: 0.6360 (ptt90) REVERT: D 63 MET cc_start: 0.9601 (mmp) cc_final: 0.9400 (mmm) REVERT: D 70 ILE cc_start: 0.9565 (mm) cc_final: 0.9345 (mm) REVERT: E 51 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8126 (mt-10) REVERT: E 95 GLU cc_start: 0.8737 (tp30) cc_final: 0.8256 (tt0) REVERT: E 106 GLU cc_start: 0.9131 (pm20) cc_final: 0.8815 (pm20) REVERT: F 61 VAL cc_start: 0.9708 (t) cc_final: 0.9218 (t) REVERT: F 64 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8748 (mt-10) REVERT: G 88 ILE cc_start: 0.9845 (tp) cc_final: 0.9581 (pt) REVERT: G 94 LEU cc_start: 0.9744 (mt) cc_final: 0.9521 (tt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1261 time to fit residues: 40.3146 Evaluate side-chains 156 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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: 0.0470 chunk 112 optimal weight: 50.0000 chunk 308 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 217 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 overall best weight: 4.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 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 = 0.4451 r_free = 0.4451 target = 0.128688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.089405 restraints weight = 98036.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.091152 restraints weight = 53359.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.092616 restraints weight = 35398.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.093762 restraints weight = 26309.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.094545 restraints weight = 20775.587| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 24183 Z= 0.264 Angle : 0.619 16.398 34337 Z= 0.354 Chirality : 0.040 0.236 4204 Planarity : 0.004 0.048 3714 Dihedral : 25.229 88.815 6163 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: 1.35 (0.16), residues: 3004 helix: 1.91 (0.12), residues: 1815 sheet: -0.22 (0.46), residues: 146 loop : -0.75 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 73 TYR 0.029 0.002 TYR D 122 PHE 0.019 0.001 PHE B 62 TRP 0.000 0.000 TRP I 764 HIS 0.008 0.002 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00565 (24183) covalent geometry : angle 0.61912 (34337) hydrogen bonds : bond 0.06699 ( 1733) hydrogen bonds : angle 3.87551 ( 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 177 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LEU cc_start: 0.8558 (pp) cc_final: 0.8343 (pp) REVERT: A 91 MET cc_start: 0.9452 (mtm) cc_final: 0.9222 (mtp) REVERT: A 106 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 110 LEU cc_start: 0.9202 (mt) cc_final: 0.8918 (mt) REVERT: A 120 ILE cc_start: 0.9575 (pt) cc_final: 0.9289 (pt) REVERT: A 121 MET cc_start: 0.8485 (ptp) cc_final: 0.7818 (mpp) REVERT: B 64 GLU cc_start: 0.9175 (mp0) cc_final: 0.8911 (pm20) REVERT: B 69 ASP cc_start: 0.9480 (m-30) cc_final: 0.9056 (m-30) REVERT: B 85 MET cc_start: 0.9489 (mmt) cc_final: 0.9272 (mmt) REVERT: C 65 GLU cc_start: 0.9081 (tt0) cc_final: 0.8738 (tp30) REVERT: C 100 ARG cc_start: 0.8540 (mmp80) cc_final: 0.8256 (mmm160) REVERT: C 113 GLN cc_start: 0.7517 (tp-100) cc_final: 0.7230 (tp-100) REVERT: C 115 VAL cc_start: 0.7785 (t) cc_final: 0.7357 (p) REVERT: D 34 ARG cc_start: 0.6829 (ptt-90) cc_final: 0.5787 (ptt180) REVERT: D 60 MET cc_start: 0.9071 (tpt) cc_final: 0.8622 (tmm) REVERT: D 70 ILE cc_start: 0.9631 (mm) cc_final: 0.9409 (mm) REVERT: D 114 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8208 (tm-30) REVERT: E 51 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8082 (mt-10) REVERT: E 95 GLU cc_start: 0.8866 (tp30) cc_final: 0.8426 (tt0) REVERT: F 64 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8910 (mt-10) REVERT: F 71 VAL cc_start: 0.9824 (m) cc_final: 0.9534 (p) REVERT: F 85 MET cc_start: 0.9196 (tpt) cc_final: 0.8940 (tpp) REVERT: G 113 GLN cc_start: 0.8536 (tp40) cc_final: 0.8314 (tp-100) REVERT: H 66 PHE cc_start: 0.9536 (t80) cc_final: 0.9292 (t80) REVERT: H 114 GLU cc_start: 0.8690 (mp0) cc_final: 0.8294 (mp0) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1163 time to fit residues: 35.9740 Evaluate side-chains 153 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 0.9990 chunk 322 optimal weight: 3.9990 chunk 259 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 103 optimal weight: 40.0000 chunk 239 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 chunk 293 optimal weight: 0.4980 chunk 88 optimal weight: 0.0980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** 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 = 0.4573 r_free = 0.4573 target = 0.152535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.107219 restraints weight = 199818.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.106986 restraints weight = 92111.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.107353 restraints weight = 58518.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.107189 restraints weight = 41879.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.107305 restraints weight = 36378.432| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 24183 Z= 0.148 Angle : 0.553 13.440 34337 Z= 0.313 Chirality : 0.038 0.196 4204 Planarity : 0.004 0.043 3714 Dihedral : 25.157 87.342 6163 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.68 (0.16), residues: 3004 helix: 2.17 (0.12), residues: 1813 sheet: 0.15 (0.47), residues: 143 loop : -0.66 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 93 TYR 0.016 0.001 TYR D 122 PHE 0.010 0.001 PHE E 68 TRP 0.000 0.000 TRP I 764 HIS 0.009 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00317 (24183) covalent geometry : angle 0.55295 (34337) hydrogen bonds : bond 0.03642 ( 1733) hydrogen bonds : angle 3.51061 ( 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 185 residues out of total 2690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.750 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 61 LEU cc_start: 0.8230 (pp) cc_final: 0.7990 (pp) REVERT: A 91 MET cc_start: 0.9558 (mtm) cc_final: 0.9256 (mtp) REVERT: A 106 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 110 LEU cc_start: 0.9379 (mt) cc_final: 0.9004 (mt) REVERT: A 120 ILE cc_start: 0.9650 (pt) cc_final: 0.9443 (pt) REVERT: A 121 MET cc_start: 0.8795 (ptp) cc_final: 0.7945 (mpp) REVERT: B 68 ARG cc_start: 0.9436 (ttp-110) cc_final: 0.9144 (ttm110) REVERT: B 85 MET cc_start: 0.9284 (mmt) cc_final: 0.9045 (mmt) REVERT: C 65 GLU cc_start: 0.9055 (tt0) cc_final: 0.8738 (tp30) REVERT: C 100 ARG cc_start: 0.8535 (mmp80) cc_final: 0.8227 (mmm160) REVERT: C 113 GLN cc_start: 0.7269 (tp-100) cc_final: 0.7035 (tp-100) REVERT: C 115 VAL cc_start: 0.7673 (t) cc_final: 0.7247 (p) REVERT: D 34 ARG cc_start: 0.7007 (ptt-90) cc_final: 0.5954 (ptt180) REVERT: D 70 ILE cc_start: 0.9566 (mm) cc_final: 0.9357 (mm) REVERT: E 51 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8022 (mt-10) REVERT: E 95 GLU cc_start: 0.8709 (tp30) cc_final: 0.8242 (tt0) REVERT: F 61 VAL cc_start: 0.9703 (t) cc_final: 0.9231 (t) REVERT: F 64 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8747 (mt-10) REVERT: F 85 MET cc_start: 0.8960 (tpt) cc_final: 0.8736 (tpp) REVERT: H 60 MET cc_start: 0.9356 (tpp) cc_final: 0.9055 (tpp) REVERT: H 114 GLU cc_start: 0.8369 (mp0) cc_final: 0.8150 (mp0) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1243 time to fit residues: 39.7035 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 : 0.801 ------------------------------------------------------------------------------- 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: 5.9990 chunk 88 optimal weight: 30.0000 chunk 102 optimal weight: 0.5980 chunk 206 optimal weight: 20.0000 chunk 145 optimal weight: 0.0270 chunk 233 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 180 optimal weight: 20.0000 chunk 222 optimal weight: 40.0000 chunk 36 optimal weight: 0.9980 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** 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 = 0.4573 r_free = 0.4573 target = 0.152509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.109649 restraints weight = 197334.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.108168 restraints weight = 96407.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.108534 restraints weight = 49417.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.108547 restraints weight = 37003.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.108679 restraints weight = 32356.671| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 24183 Z= 0.157 Angle : 0.538 12.968 34337 Z= 0.306 Chirality : 0.038 0.148 4204 Planarity : 0.004 0.042 3714 Dihedral : 24.832 87.118 6163 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.16), residues: 3004 helix: 2.36 (0.12), residues: 1811 sheet: 0.25 (0.47), residues: 142 loop : -0.54 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 41 TYR 0.015 0.001 TYR D 122 PHE 0.010 0.001 PHE E 105 TRP 0.000 0.000 TRP I 764 HIS 0.009 0.002 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00337 (24183) covalent geometry : angle 0.53765 (34337) hydrogen bonds : bond 0.03939 ( 1733) hydrogen bonds : angle 3.38433 ( 4629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7155.34 seconds wall clock time: 121 minutes 52.25 seconds (7312.25 seconds total)