Starting phenix.real_space_refine on Fri Jul 3 23:30:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21wa_68034/07_2026/21wa_68034.cif Found real_map, /net/cci-nas-00/data/ceres_data/21wa_68034/07_2026/21wa_68034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21wa_68034/07_2026/21wa_68034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21wa_68034/07_2026/21wa_68034.map" model { file = "/net/cci-nas-00/data/ceres_data/21wa_68034/07_2026/21wa_68034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21wa_68034/07_2026/21wa_68034.cif" } resolution = 3.7 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= -0.000 sd= 0.003 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: 8 Type Number sf(0) Gaussians P 276 5.49 5 Mg 1 5.21 5 S 38 5.16 5 Be 1 3.05 5 C 9673 2.51 5 N 3092 2.21 5 O 3617 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16701 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 756 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 858 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 4936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4936 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 19, 'TRANS': 583} Chain breaks: 5 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 2791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2791 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "Y" Number of atoms: 2826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2826 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.42, per 1000 atoms: 0.20 Number of scatterers: 16701 At special positions: 0 Unit cell: (106.7, 121, 156.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 38 16.00 P 276 15.00 Mg 1 11.99 F 3 9.00 O 3617 8.00 N 3092 7.00 C 9673 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 508.6 milliseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2588 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 10 sheets defined 62.7% alpha, 4.6% beta 98 base pairs and 230 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.970A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 85 through 112 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.818A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.931A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.492A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.596A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 removed outlier: 3.534A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 105 through 123 removed outlier: 3.617A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 56 removed outlier: 3.673A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.871A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.689A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.820A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.907A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.677A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.662A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.940A pdb=" N ALA H 97 " --> pdb=" O GLU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.519A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 573 removed outlier: 3.521A pdb=" N TYR I 552 " --> pdb=" O LYS I 548 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN I 555 " --> pdb=" O ALA I 551 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN I 556 " --> pdb=" O TYR I 552 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP I 558 " --> pdb=" O LEU I 554 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL I 561 " --> pdb=" O THR I 557 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA I 562 " --> pdb=" O ASP I 558 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 736 removed outlier: 3.785A pdb=" N HIS I 736 " --> pdb=" O TYR I 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 732 through 736' Processing helix chain 'I' and resid 755 through 771 Processing helix chain 'I' and resid 786 through 799 Processing helix chain 'I' and resid 811 through 825 removed outlier: 4.667A pdb=" N SER I 816 " --> pdb=" O LEU I 812 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASN I 817 " --> pdb=" O SER I 813 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA I 819 " --> pdb=" O LEU I 815 " (cutoff:3.500A) Processing helix chain 'I' and resid 837 through 843 Processing helix chain 'I' and resid 844 through 851 Processing helix chain 'I' and resid 859 through 866 removed outlier: 3.662A pdb=" N ILE I 863 " --> pdb=" O THR I 859 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE I 864 " --> pdb=" O TYR I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 866 through 871 Processing helix chain 'I' and resid 882 through 888 removed outlier: 3.799A pdb=" N ARG I 885 " --> pdb=" O GLU I 882 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN I 888 " --> pdb=" O ARG I 885 " (cutoff:3.500A) Processing helix chain 'I' and resid 891 through 899 Processing helix chain 'I' and resid 918 through 929 Processing helix chain 'I' and resid 960 through 972 removed outlier: 3.990A pdb=" N LEU I 972 " --> pdb=" O LEU I 968 " (cutoff:3.500A) Processing helix chain 'I' and resid 980 through 985 removed outlier: 3.634A pdb=" N VAL I 984 " --> pdb=" O LEU I 980 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1015 removed outlier: 4.006A pdb=" N ARG I1009 " --> pdb=" O ARG I1005 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS I1010 " --> pdb=" O VAL I1006 " (cutoff:3.500A) Processing helix chain 'I' and resid 1037 through 1048 removed outlier: 3.503A pdb=" N GLN I1041 " --> pdb=" O ASN I1037 " (cutoff:3.500A) Processing helix chain 'I' and resid 1049 through 1053 removed outlier: 3.829A pdb=" N PHE I1052 " --> pdb=" O PRO I1049 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN I1053 " --> pdb=" O TYR I1050 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1049 through 1053' Processing helix chain 'I' and resid 1054 through 1063 Processing helix chain 'I' and resid 1073 through 1079 removed outlier: 4.255A pdb=" N SER I1079 " --> pdb=" O LEU I1075 " (cutoff:3.500A) Processing helix chain 'I' and resid 1079 through 1095 Proline residue: I1090 - end of helix removed outlier: 3.576A pdb=" N THR I1095 " --> pdb=" O LYS I1091 " (cutoff:3.500A) Processing helix chain 'I' and resid 1105 through 1120 removed outlier: 3.665A pdb=" N MET I1109 " --> pdb=" O MET I1105 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP I1114 " --> pdb=" O THR I1110 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR I1115 " --> pdb=" O ILE I1111 " (cutoff:3.500A) Processing helix chain 'I' and resid 1133 through 1144 removed outlier: 4.391A pdb=" N MET I1137 " --> pdb=" O GLU I1133 " (cutoff:3.500A) Processing helix chain 'I' and resid 1179 through 1188 removed outlier: 3.851A pdb=" N ASP I1183 " --> pdb=" O ASN I1179 " (cutoff:3.500A) Processing helix chain 'I' and resid 1189 through 1191 No H-bonds generated for 'chain 'I' and resid 1189 through 1191' Processing helix chain 'I' and resid 1209 through 1227 removed outlier: 4.265A pdb=" N LYS I1213 " --> pdb=" O SER I1209 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL I1224 " --> pdb=" O TYR I1220 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS I1227 " --> pdb=" O ASN I1223 " (cutoff:3.500A) Processing helix chain 'I' and resid 1241 through 1255 removed outlier: 3.615A pdb=" N ALA I1245 " --> pdb=" O HIS I1241 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA I1249 " --> pdb=" O ALA I1245 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE I1250 " --> pdb=" O PHE I1246 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU I1251 " --> pdb=" O LEU I1247 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU I1252 " --> pdb=" O GLN I1248 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU I1255 " --> pdb=" O LEU I1251 " (cutoff:3.500A) Processing helix chain 'I' and resid 1300 through 1307 removed outlier: 4.187A pdb=" N GLN I1304 " --> pdb=" O GLU I1300 " (cutoff:3.500A) Processing helix chain 'I' and resid 1309 through 1317 removed outlier: 3.580A pdb=" N PHE I1316 " --> pdb=" O GLU I1312 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET I1317 " --> pdb=" O PHE I1313 " (cutoff:3.500A) Processing helix chain 'I' and resid 1319 through 1330 removed outlier: 3.771A pdb=" N ASN I1330 " --> pdb=" O GLU I1326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.816A pdb=" N THR B 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.376A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.887A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.695A pdb=" N THR F 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.459A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'I' and resid 776 through 777 removed outlier: 6.561A pdb=" N MET I 878 " --> pdb=" O LEU I 907 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU I 909 " --> pdb=" O MET I 878 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL I 880 " --> pdb=" O LEU I 909 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU I 807 " --> pdb=" O ILE I 879 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE I 808 " --> pdb=" O THR I 858 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL I 832 " --> pdb=" O LEU I 857 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 992 through 998 removed outlier: 6.986A pdb=" N VAL I1171 " --> pdb=" O LEU I1202 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N LEU I1204 " --> pdb=" O VAL I1171 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE I1173 " --> pdb=" O LEU I1204 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N THR I1206 " --> pdb=" O ILE I1173 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL I1099 " --> pdb=" O PHE I1152 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU I1154 " --> pdb=" O VAL I1099 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU I1101 " --> pdb=" O LEU I1154 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU I1124 " --> pdb=" O LEU I1153 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N SER I1155 " --> pdb=" O LEU I1124 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N LEU I1126 " --> pdb=" O SER I1155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 1016 through 1018 559 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 253 hydrogen bonds 494 hydrogen bond angles 0 basepair planarities 98 basepair parallelities 230 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3628 1.33 - 1.45: 4838 1.45 - 1.57: 8476 1.57 - 1.69: 549 1.69 - 1.81: 68 Bond restraints: 17559 Sorted by residual: bond pdb=" C3' DA Y 60 " pdb=" C2' DA Y 60 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC Y 104 " pdb=" C2' DC Y 104 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT Y 15 " pdb=" C2' DT Y 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.93e+00 bond pdb=" C3' DC X 45 " pdb=" C2' DC X 45 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.27e+00 bond pdb=" C3' DC Y 126 " pdb=" C2' DC Y 126 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.89e+00 ... (remaining 17554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 23410 1.40 - 2.81: 1351 2.81 - 4.21: 76 4.21 - 5.62: 23 5.62 - 7.02: 6 Bond angle restraints: 24866 Sorted by residual: angle pdb=" N ILE A 112 " pdb=" CA ILE A 112 " pdb=" C ILE A 112 " ideal model delta sigma weight residual 112.83 107.33 5.50 9.90e-01 1.02e+00 3.09e+01 angle pdb=" O4' DA Y 44 " pdb=" C4' DA Y 44 " pdb=" C3' DA Y 44 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.47e+01 angle pdb=" N3 DT X 87 " pdb=" C4 DT X 87 " pdb=" O4 DT X 87 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT X 75 " pdb=" C4 DT X 75 " pdb=" O4 DT X 75 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT X 35 " pdb=" C4 DT X 35 " pdb=" O4 DT X 35 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 24861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 8548 34.34 - 68.68: 1306 68.68 - 103.01: 46 103.01 - 137.35: 0 137.35 - 171.69: 3 Dihedral angle restraints: 9903 sinusoidal: 5902 harmonic: 4001 Sorted by residual: dihedral pdb=" O2A ADP I1802 " pdb=" O3A ADP I1802 " pdb=" PA ADP I1802 " pdb=" PB ADP I1802 " ideal model delta sinusoidal sigma weight residual -60.00 -159.53 99.54 1 2.00e+01 2.50e-03 2.80e+01 dihedral pdb=" C4' DT Y 15 " pdb=" C3' DT Y 15 " pdb=" O3' DT Y 15 " pdb=" P DC Y 16 " ideal model delta sinusoidal sigma weight residual 220.00 48.31 171.69 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG Y 94 " pdb=" C3' DG Y 94 " pdb=" O3' DG Y 94 " pdb=" P DG Y 95 " ideal model delta sinusoidal sigma weight residual 220.00 58.08 161.92 1 3.50e+01 8.16e-04 1.53e+01 ... (remaining 9900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1677 0.032 - 0.065: 746 0.065 - 0.097: 274 0.097 - 0.129: 107 0.129 - 0.161: 5 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C3' DG Y 94 " pdb=" C4' DG Y 94 " pdb=" O3' DG Y 94 " pdb=" C2' DG Y 94 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" C3' DT Y 15 " pdb=" C4' DT Y 15 " pdb=" O3' DT Y 15 " pdb=" C2' DT Y 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" C3' DC Y 126 " pdb=" C4' DC Y 126 " pdb=" O3' DC Y 126 " pdb=" C2' DC Y 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2806 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA Y 91 " -0.025 2.00e-02 2.50e+03 1.17e-02 3.73e+00 pdb=" N9 DA Y 91 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA Y 91 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA Y 91 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA Y 91 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA Y 91 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA Y 91 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA Y 91 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA Y 91 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA Y 91 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA Y 91 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY I 804 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO I 805 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 805 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 805 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 131 " 0.023 2.00e-02 2.50e+03 9.66e-03 2.57e+00 pdb=" N9 DA X 131 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA X 131 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA X 131 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA X 131 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA X 131 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA X 131 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA X 131 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA X 131 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA X 131 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA X 131 " -0.003 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 199 2.64 - 3.20: 14515 3.20 - 3.77: 28208 3.77 - 4.33: 37525 4.33 - 4.90: 56843 Nonbonded interactions: 137290 Sorted by model distance: nonbonded pdb=" O2 DC X 143 " pdb=" N2 DG Y 5 " model vdw 2.069 2.496 nonbonded pdb=" N2 DG X 148 " pdb=" O2 DC Y 0 " model vdw 2.075 2.496 nonbonded pdb=" O2 DC X 95 " pdb=" N2 DG Y 53 " model vdw 2.077 2.496 nonbonded pdb=" OD2 ASP I 881 " pdb="MG MG I1801 " model vdw 2.152 2.170 nonbonded pdb=" OE1 GLN I1104 " pdb=" OG1 THR I1156 " model vdw 2.214 3.040 ... (remaining 137285 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 22 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 117) } ncs_group { reference = (chain 'D' and resid 31 through 124) 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: 3.130 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.220 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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: 23.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.005 0.039 17559 Z= 0.423 Angle : 0.686 7.019 24866 Z= 0.565 Chirality : 0.043 0.161 2809 Planarity : 0.004 0.041 2196 Dihedral : 24.504 171.690 7315 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.11 % Allowed : 8.51 % Favored : 90.38 % 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: 0.14 (0.23), residues: 1346 helix: 1.16 (0.19), residues: 788 sheet: -0.11 (0.69), residues: 64 loop : -1.66 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 966 TYR 0.020 0.001 TYR I 560 PHE 0.012 0.001 PHE I1152 TRP 0.012 0.001 TRP I 922 HIS 0.003 0.001 HIS I 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.42 (17559) covalent geometry : angle 0.68646 / 0.56 (24866) hydrogen bonds : bond 0.12470 / 8.80 ( 812) hydrogen bonds : angle 4.57381 / 3.28 ( 2153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7324 (mtp-110) REVERT: B 27 GLN cc_start: 0.8007 (mp10) cc_final: 0.7703 (mp10) REVERT: D 86 ARG cc_start: 0.8334 (mpt180) cc_final: 0.8029 (mpt180) REVERT: G 104 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8166 (mm-40) REVERT: H 47 GLN cc_start: 0.8266 (tt0) cc_final: 0.8023 (tt0) REVERT: H 59 MET cc_start: 0.8525 (tpp) cc_final: 0.8184 (tpp) REVERT: I 972 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5248 (pp) REVERT: I 1076 TYR cc_start: 0.6876 (t80) cc_final: 0.6367 (t80) outliers start: 13 outliers final: 9 residues processed: 174 average time/residue: 0.1809 time to fit residues: 43.7414 Evaluate side-chains 143 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0030 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.0070 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 0.3408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 68 GLN A 85 GLN A 125 GLN B 75 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN H 109 HIS I 770 ASN I 788 GLN I 847 GLN I 941 GLN I1012 GLN I1062 HIS I1097 HIS ** I1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1253 HIS I1330 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.185089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172914 restraints weight = 19753.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.151333 restraints weight = 47352.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.147594 restraints weight = 41532.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.146991 restraints weight = 39919.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.147780 restraints weight = 31287.449| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17559 Z= 0.141 Angle : 0.599 9.287 24866 Z= 0.337 Chirality : 0.043 0.290 2809 Planarity : 0.004 0.040 2196 Dihedral : 28.618 174.615 4546 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.21 % Allowed : 11.66 % Favored : 86.13 % 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: 0.31 (0.23), residues: 1346 helix: 1.29 (0.19), residues: 801 sheet: 0.05 (0.69), residues: 64 loop : -1.68 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I1323 TYR 0.022 0.001 TYR I1076 PHE 0.009 0.001 PHE I1152 TRP 0.012 0.001 TRP I 922 HIS 0.004 0.001 HIS I 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (17559) covalent geometry : angle 0.59932 / 0.34 (24866) hydrogen bonds : bond 0.05809 / 4.08 ( 812) hydrogen bonds : angle 3.59413 / 2.58 ( 2153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 86 ARG cc_start: 0.8318 (mpt180) cc_final: 0.7947 (mpt180) REVERT: F 84 MET cc_start: 0.8925 (tpp) cc_final: 0.8587 (tpt) REVERT: H 59 MET cc_start: 0.8559 (tpp) cc_final: 0.8192 (tpp) REVERT: H 62 MET cc_start: 0.9026 (mmm) cc_final: 0.8816 (mmm) REVERT: I 763 GLU cc_start: 0.4596 (tt0) cc_final: 0.4241 (tt0) REVERT: I 792 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7485 (tp) REVERT: I 972 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.4953 (pp) REVERT: I 1011 MET cc_start: 0.7583 (tpp) cc_final: 0.6806 (ttt) outliers start: 26 outliers final: 15 residues processed: 171 average time/residue: 0.1882 time to fit residues: 44.1211 Evaluate side-chains 152 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 792 LEU Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1299 ASP Chi-restraints excluded: chain I residue 1310 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 2 optimal weight: 0.0170 chunk 73 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 80 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 89 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I1062 HIS I1208 ASN I1226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.186016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.174082 restraints weight = 19887.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152012 restraints weight = 47224.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.147884 restraints weight = 41747.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.147946 restraints weight = 38709.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.148186 restraints weight = 31798.199| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 17559 Z= 0.129 Angle : 0.557 8.951 24866 Z= 0.318 Chirality : 0.041 0.296 2809 Planarity : 0.004 0.057 2196 Dihedral : 28.505 175.447 4546 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.47 % Allowed : 13.19 % Favored : 84.34 % 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: 0.46 (0.23), residues: 1346 helix: 1.43 (0.19), residues: 808 sheet: 0.17 (0.67), residues: 64 loop : -1.70 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I1325 TYR 0.018 0.001 TYR I 560 PHE 0.009 0.001 PHE I1152 TRP 0.009 0.001 TRP I 922 HIS 0.005 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (17559) covalent geometry : angle 0.55719 / 0.32 (24866) hydrogen bonds : bond 0.05221 / 3.66 ( 812) hydrogen bonds : angle 3.39116 / 2.43 ( 2153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 86 ARG cc_start: 0.8371 (mpt180) cc_final: 0.8004 (mpt180) REVERT: F 84 MET cc_start: 0.8906 (tpp) cc_final: 0.8612 (tpt) REVERT: H 62 MET cc_start: 0.9037 (mmm) cc_final: 0.8835 (mmm) REVERT: I 792 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7572 (tp) REVERT: I 972 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5008 (pp) outliers start: 29 outliers final: 14 residues processed: 172 average time/residue: 0.1783 time to fit residues: 43.0103 Evaluate side-chains 153 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 792 LEU Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 918 LEU Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1299 ASP Chi-restraints excluded: chain I residue 1310 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 900 HIS I1062 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.184172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.172245 restraints weight = 19731.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.149038 restraints weight = 46315.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.145207 restraints weight = 38196.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.145181 restraints weight = 38381.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.145542 restraints weight = 28309.039| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17559 Z= 0.132 Angle : 0.562 9.694 24866 Z= 0.316 Chirality : 0.041 0.316 2809 Planarity : 0.004 0.038 2196 Dihedral : 28.526 177.510 4546 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.13 % Allowed : 14.47 % Favored : 83.40 % 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: 0.51 (0.23), residues: 1346 helix: 1.47 (0.19), residues: 808 sheet: 0.27 (0.69), residues: 64 loop : -1.70 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I1323 TYR 0.020 0.001 TYR I1123 PHE 0.008 0.001 PHE I1152 TRP 0.010 0.001 TRP I 922 HIS 0.005 0.001 HIS I 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (17559) covalent geometry : angle 0.56174 / 0.32 (24866) hydrogen bonds : bond 0.05174 / 3.62 ( 812) hydrogen bonds : angle 3.35286 / 2.40 ( 2153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8615 (m-80) cc_final: 0.8262 (m-80) REVERT: B 27 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7413 (mp10) REVERT: D 86 ARG cc_start: 0.8388 (mpt180) cc_final: 0.8061 (mpt180) REVERT: F 84 MET cc_start: 0.8908 (tpp) cc_final: 0.8613 (tpt) REVERT: I 792 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7513 (tp) REVERT: I 801 ARG cc_start: 0.7417 (mmm160) cc_final: 0.6937 (tpm170) REVERT: I 972 LEU cc_start: 0.5925 (OUTLIER) cc_final: 0.4997 (pp) REVERT: I 1011 MET cc_start: 0.7299 (tpp) cc_final: 0.6699 (ttt) REVERT: I 1105 MET cc_start: 0.7751 (mtt) cc_final: 0.7436 (mtt) REVERT: I 1366 MET cc_start: 0.5945 (pmm) cc_final: 0.4940 (ptt) outliers start: 25 outliers final: 16 residues processed: 161 average time/residue: 0.1943 time to fit residues: 42.7724 Evaluate side-chains 156 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 792 LEU Chi-restraints excluded: chain I residue 869 ILE Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1299 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 80 optimal weight: 0.0670 chunk 116 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 75 HIS ** 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 = 0.4023 r_free = 0.4023 target = 0.184287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.171831 restraints weight = 19781.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151644 restraints weight = 49275.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.146957 restraints weight = 44584.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.146440 restraints weight = 41899.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.146860 restraints weight = 32874.691| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17559 Z= 0.130 Angle : 0.562 10.935 24866 Z= 0.314 Chirality : 0.041 0.314 2809 Planarity : 0.004 0.036 2196 Dihedral : 28.519 178.656 4546 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.13 % Allowed : 14.72 % Favored : 83.15 % 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: 0.55 (0.23), residues: 1346 helix: 1.51 (0.19), residues: 808 sheet: 0.35 (0.69), residues: 64 loop : -1.72 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.018 0.001 TYR I1123 PHE 0.008 0.001 PHE I1152 TRP 0.010 0.001 TRP I 922 HIS 0.011 0.001 HIS I 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (17559) covalent geometry : angle 0.56160 / 0.31 (24866) hydrogen bonds : bond 0.05100 / 3.57 ( 812) hydrogen bonds : angle 3.29737 / 2.36 ( 2153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: D 86 ARG cc_start: 0.8373 (mpt180) cc_final: 0.8004 (mpt180) REVERT: F 84 MET cc_start: 0.8897 (tpp) cc_final: 0.8620 (tpt) REVERT: G 93 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9281 (mt) REVERT: H 59 MET cc_start: 0.8246 (tpp) cc_final: 0.8005 (tpp) REVERT: I 792 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7578 (tp) REVERT: I 972 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5241 (pp) REVERT: I 1011 MET cc_start: 0.7261 (tpp) cc_final: 0.6729 (ttt) REVERT: I 1105 MET cc_start: 0.7792 (mtt) cc_final: 0.7520 (mtt) REVERT: I 1366 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5100 (ptt) outliers start: 25 outliers final: 16 residues processed: 159 average time/residue: 0.1730 time to fit residues: 38.5138 Evaluate side-chains 157 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 792 LEU Chi-restraints excluded: chain I residue 869 ILE Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1003 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1210 VAL Chi-restraints excluded: chain I residue 1299 ASP Chi-restraints excluded: chain I residue 1366 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 149 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 154 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 803 ASN I1062 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.182534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.170532 restraints weight = 19819.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.147718 restraints weight = 47403.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.144539 restraints weight = 44232.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.143713 restraints weight = 38639.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.143858 restraints weight = 29630.088| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17559 Z= 0.158 Angle : 0.595 14.607 24866 Z= 0.326 Chirality : 0.042 0.344 2809 Planarity : 0.004 0.046 2196 Dihedral : 28.697 178.995 4544 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.64 % Allowed : 14.38 % Favored : 82.98 % 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: 0.45 (0.23), residues: 1346 helix: 1.43 (0.19), residues: 808 sheet: 0.30 (0.69), residues: 64 loop : -1.76 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 99 TYR 0.017 0.001 TYR I 560 PHE 0.010 0.001 PHE A 84 TRP 0.012 0.001 TRP I 922 HIS 0.005 0.001 HIS I 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (17559) covalent geometry : angle 0.59503 / 0.33 (24866) hydrogen bonds : bond 0.05447 / 3.80 ( 812) hydrogen bonds : angle 3.35333 / 2.40 ( 2153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8100 (mp-120) cc_final: 0.7654 (tm-30) REVERT: C 92 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: D 86 ARG cc_start: 0.8414 (mpt180) cc_final: 0.8061 (mpt180) REVERT: F 84 MET cc_start: 0.8907 (tpp) cc_final: 0.8670 (tpt) REVERT: G 34 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8796 (mp) REVERT: G 58 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8657 (mm) REVERT: G 104 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8050 (mm110) REVERT: I 765 LEU cc_start: 0.6090 (pp) cc_final: 0.5401 (mt) REVERT: I 792 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7636 (tp) REVERT: I 972 LEU cc_start: 0.6179 (OUTLIER) cc_final: 0.5239 (pp) REVERT: I 1011 MET cc_start: 0.7270 (tpp) cc_final: 0.6736 (ttt) REVERT: I 1105 MET cc_start: 0.7946 (mtt) cc_final: 0.7683 (mtt) REVERT: I 1327 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: I 1366 MET cc_start: 0.6170 (OUTLIER) cc_final: 0.5165 (ptt) outliers start: 31 outliers final: 21 residues processed: 163 average time/residue: 0.1784 time to fit residues: 40.6447 Evaluate side-chains 160 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 792 LEU Chi-restraints excluded: chain I residue 869 ILE Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1003 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1210 VAL Chi-restraints excluded: chain I residue 1299 ASP Chi-restraints excluded: chain I residue 1327 GLU Chi-restraints excluded: chain I residue 1366 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 30 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 67 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1062 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.183273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171061 restraints weight = 19884.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.149179 restraints weight = 49264.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.144905 restraints weight = 41847.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.144900 restraints weight = 39700.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.145177 restraints weight = 30835.961| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17559 Z= 0.133 Angle : 0.568 12.374 24866 Z= 0.315 Chirality : 0.041 0.322 2809 Planarity : 0.004 0.040 2196 Dihedral : 28.598 179.047 4542 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.72 % Allowed : 14.98 % Favored : 82.30 % 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: 0.51 (0.23), residues: 1346 helix: 1.50 (0.19), residues: 808 sheet: 0.34 (0.69), residues: 64 loop : -1.78 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I1325 TYR 0.017 0.001 TYR I 560 PHE 0.008 0.001 PHE I1152 TRP 0.011 0.001 TRP I 922 HIS 0.004 0.001 HIS I 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (17559) covalent geometry : angle 0.56850 / 0.31 (24866) hydrogen bonds : bond 0.05135 / 3.58 ( 812) hydrogen bonds : angle 3.27076 / 2.34 ( 2153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.7995 (mp-120) cc_final: 0.7750 (mp10) REVERT: C 92 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: D 86 ARG cc_start: 0.8381 (mpt180) cc_final: 0.8028 (mpt180) REVERT: F 84 MET cc_start: 0.8897 (tpp) cc_final: 0.8658 (tpt) REVERT: G 58 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8626 (mm) REVERT: G 104 GLN cc_start: 0.8484 (mm-40) cc_final: 0.8103 (mm110) REVERT: I 765 LEU cc_start: 0.5982 (pp) cc_final: 0.5335 (mt) REVERT: I 792 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7647 (tp) REVERT: I 801 ARG cc_start: 0.7480 (mmm160) cc_final: 0.7005 (tpm170) REVERT: I 972 LEU cc_start: 0.6243 (OUTLIER) cc_final: 0.5339 (pp) REVERT: I 1011 MET cc_start: 0.7265 (tpp) cc_final: 0.6739 (ttt) REVERT: I 1105 MET cc_start: 0.8013 (mtt) cc_final: 0.7639 (mtt) REVERT: I 1327 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6272 (pm20) REVERT: I 1366 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5084 (ptt) outliers start: 32 outliers final: 20 residues processed: 163 average time/residue: 0.1709 time to fit residues: 39.4256 Evaluate side-chains 157 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 792 LEU Chi-restraints excluded: chain I residue 869 ILE Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1003 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1210 VAL Chi-restraints excluded: chain I residue 1299 ASP Chi-restraints excluded: chain I residue 1327 GLU Chi-restraints excluded: chain I residue 1337 LEU Chi-restraints excluded: chain I residue 1366 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1062 HIS I1226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.182214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.168387 restraints weight = 19898.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.150297 restraints weight = 57234.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.146683 restraints weight = 49593.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.144959 restraints weight = 37479.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.145097 restraints weight = 33655.717| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17559 Z= 0.153 Angle : 0.586 11.777 24866 Z= 0.321 Chirality : 0.042 0.343 2809 Planarity : 0.004 0.047 2196 Dihedral : 28.703 179.621 4542 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.64 % Allowed : 15.40 % Favored : 81.96 % 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: 0.46 (0.23), residues: 1346 helix: 1.46 (0.19), residues: 807 sheet: 0.36 (0.69), residues: 64 loop : -1.78 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I1325 TYR 0.016 0.001 TYR I 560 PHE 0.014 0.001 PHE H 70 TRP 0.012 0.001 TRP I 922 HIS 0.004 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (17559) covalent geometry : angle 0.58605 / 0.32 (24866) hydrogen bonds : bond 0.05338 / 3.72 ( 812) hydrogen bonds : angle 3.30803 / 2.36 ( 2153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8030 (mp-120) cc_final: 0.7739 (mp10) REVERT: C 92 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: D 86 ARG cc_start: 0.8383 (mpt180) cc_final: 0.8043 (mpt180) REVERT: F 84 MET cc_start: 0.8906 (tpp) cc_final: 0.8679 (tpt) REVERT: G 58 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8615 (mm) REVERT: G 104 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8113 (mm110) REVERT: H 59 MET cc_start: 0.8478 (tpp) cc_final: 0.8155 (mmm) REVERT: I 765 LEU cc_start: 0.5906 (pp) cc_final: 0.5303 (mt) REVERT: I 801 ARG cc_start: 0.7489 (mmm160) cc_final: 0.7090 (tpm170) REVERT: I 972 LEU cc_start: 0.6322 (OUTLIER) cc_final: 0.5402 (pp) REVERT: I 1011 MET cc_start: 0.7325 (tpp) cc_final: 0.6694 (ttt) REVERT: I 1105 MET cc_start: 0.8077 (mtt) cc_final: 0.7718 (mtt) REVERT: I 1317 MET cc_start: 0.6642 (mmp) cc_final: 0.6161 (mmm) REVERT: I 1327 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6038 (pm20) REVERT: I 1366 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5142 (ptt) outliers start: 31 outliers final: 20 residues processed: 158 average time/residue: 0.1727 time to fit residues: 38.3637 Evaluate side-chains 152 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 869 ILE Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1003 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1210 VAL Chi-restraints excluded: chain I residue 1299 ASP Chi-restraints excluded: chain I residue 1327 GLU Chi-restraints excluded: chain I residue 1366 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 0.0040 chunk 121 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 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 = 0.4017 r_free = 0.4017 target = 0.183733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.152974 restraints weight = 19993.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.152113 restraints weight = 26676.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.151866 restraints weight = 24589.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.151857 restraints weight = 21477.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.151883 restraints weight = 18179.192| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17559 Z= 0.134 Angle : 0.584 13.699 24866 Z= 0.319 Chirality : 0.041 0.330 2809 Planarity : 0.004 0.046 2196 Dihedral : 28.660 178.959 4542 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.38 % Allowed : 15.57 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.23), residues: 1346 helix: 1.50 (0.19), residues: 808 sheet: 0.35 (0.69), residues: 64 loop : -1.77 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 801 TYR 0.016 0.001 TYR I 560 PHE 0.012 0.001 PHE H 70 TRP 0.010 0.001 TRP I 922 HIS 0.004 0.001 HIS I 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (17559) covalent geometry : angle 0.58376 / 0.32 (24866) hydrogen bonds : bond 0.05175 / 3.60 ( 812) hydrogen bonds : angle 3.30104 / 2.36 ( 2153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: B 92 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.8024 (ttp80) REVERT: C 92 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: D 86 ARG cc_start: 0.8359 (mpt180) cc_final: 0.8019 (mpt180) REVERT: F 84 MET cc_start: 0.8850 (tpp) cc_final: 0.8626 (tpt) REVERT: G 58 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8609 (mm) REVERT: G 104 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7998 (mm110) REVERT: H 59 MET cc_start: 0.8513 (tpp) cc_final: 0.8162 (mmm) REVERT: I 765 LEU cc_start: 0.5307 (pp) cc_final: 0.4823 (mt) REVERT: I 801 ARG cc_start: 0.7305 (mmm160) cc_final: 0.7023 (tpm170) REVERT: I 972 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5172 (pp) REVERT: I 1011 MET cc_start: 0.7338 (tpp) cc_final: 0.6672 (ttt) REVERT: I 1105 MET cc_start: 0.7999 (mtt) cc_final: 0.7629 (mtt) REVERT: I 1317 MET cc_start: 0.6193 (mmp) cc_final: 0.5781 (mmm) REVERT: I 1327 GLU cc_start: 0.5776 (OUTLIER) cc_final: 0.5523 (pm20) REVERT: I 1366 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5119 (ptt) outliers start: 28 outliers final: 18 residues processed: 153 average time/residue: 0.1850 time to fit residues: 39.4232 Evaluate side-chains 154 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 869 ILE Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1003 LEU Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1210 VAL Chi-restraints excluded: chain I residue 1299 ASP Chi-restraints excluded: chain I residue 1327 GLU Chi-restraints excluded: chain I residue 1337 LEU Chi-restraints excluded: chain I residue 1366 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 103 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 50 optimal weight: 0.0670 chunk 148 optimal weight: 9.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1062 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.182699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.169234 restraints weight = 19827.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.148867 restraints weight = 55661.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.144894 restraints weight = 47411.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.144345 restraints weight = 42278.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.144539 restraints weight = 31874.078| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17559 Z= 0.148 Angle : 0.602 12.896 24866 Z= 0.325 Chirality : 0.042 0.341 2809 Planarity : 0.004 0.049 2196 Dihedral : 28.725 177.867 4542 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.38 % Allowed : 15.91 % Favored : 81.70 % 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: 0.44 (0.23), residues: 1346 helix: 1.43 (0.19), residues: 809 sheet: 0.32 (0.69), residues: 64 loop : -1.79 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I1325 TYR 0.016 0.001 TYR I 560 PHE 0.013 0.001 PHE H 70 TRP 0.012 0.001 TRP I 922 HIS 0.006 0.001 HIS I1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (17559) covalent geometry : angle 0.60183 / 0.33 (24866) hydrogen bonds : bond 0.05308 / 3.69 ( 812) hydrogen bonds : angle 3.32813 / 2.38 ( 2153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: B 92 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8016 (ttp80) REVERT: C 92 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7893 (mp0) REVERT: D 86 ARG cc_start: 0.8398 (mpt180) cc_final: 0.8065 (mpt180) REVERT: F 84 MET cc_start: 0.8896 (tpp) cc_final: 0.8674 (tpt) REVERT: G 58 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8619 (mm) REVERT: G 104 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8042 (mm110) REVERT: H 59 MET cc_start: 0.8489 (tpp) cc_final: 0.8134 (mmm) REVERT: I 765 LEU cc_start: 0.5999 (pp) cc_final: 0.5502 (mt) REVERT: I 801 ARG cc_start: 0.7537 (mmm160) cc_final: 0.7084 (tpm170) REVERT: I 972 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.5579 (pp) REVERT: I 1011 MET cc_start: 0.7325 (tpp) cc_final: 0.6722 (ttt) REVERT: I 1105 MET cc_start: 0.8113 (mtt) cc_final: 0.7691 (mtt) REVERT: I 1366 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5239 (ptt) outliers start: 28 outliers final: 18 residues processed: 149 average time/residue: 0.1757 time to fit residues: 36.5408 Evaluate side-chains 150 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 869 ILE Chi-restraints excluded: chain I residue 875 TRP Chi-restraints excluded: chain I residue 971 VAL Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1171 VAL Chi-restraints excluded: chain I residue 1199 VAL Chi-restraints excluded: chain I residue 1201 VAL Chi-restraints excluded: chain I residue 1210 VAL Chi-restraints excluded: chain I residue 1299 ASP Chi-restraints excluded: chain I residue 1337 LEU Chi-restraints excluded: chain I residue 1366 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 129 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1062 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.181930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.169167 restraints weight = 19762.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.147621 restraints weight = 52833.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.143005 restraints weight = 49283.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.142900 restraints weight = 41120.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.143049 restraints weight = 29260.816| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17559 Z= 0.156 Angle : 0.611 13.465 24866 Z= 0.329 Chirality : 0.042 0.347 2809 Planarity : 0.004 0.048 2196 Dihedral : 28.776 177.439 4542 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.21 % Allowed : 16.34 % Favored : 81.45 % 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: 0.43 (0.23), residues: 1346 helix: 1.43 (0.19), residues: 808 sheet: 0.23 (0.69), residues: 64 loop : -1.78 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 129 TYR 0.015 0.001 TYR I 560 PHE 0.013 0.001 PHE H 70 TRP 0.011 0.001 TRP I 922 HIS 0.010 0.001 HIS I1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (17559) covalent geometry : angle 0.61065 / 0.33 (24866) hydrogen bonds : bond 0.05403 / 3.75 ( 812) hydrogen bonds : angle 3.36828 / 2.40 ( 2153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2387.82 seconds wall clock time: 42 minutes 14.73 seconds (2534.73 seconds total)