Starting phenix.real_space_refine on Thu Aug 6 19:18:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21wa_68034/08_2026/21wa_68034.cif Found real_map, /net/cci-nas-00/data/ceres_data/21wa_68034/08_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_68034/08_2026/21wa_68034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21wa_68034/08_2026/21wa_68034.map" model { file = "/net/cci-nas-00/data/ceres_data/21wa_68034/08_2026/21wa_68034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21wa_68034/08_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-2.2rc3-6140/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: 3.32, 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: 1.30 Conformation dependent library (CDL) restraints added in 544.3 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: 2.07 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: 4.08 Time building geometry restraints manager: 1.76 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: 23394 1.40 - 2.81: 1366 2.81 - 4.21: 77 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: 4.290 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.450 Find NCS groups from input model: 0.160 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.380 ------------------------------------------------------------------------------- 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 : 0.691 7.019 24866 Z= 0.569 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 0.69140 / 0.57 (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 : 0.496 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: 0.8028 (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: 0.8179 (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: 0.1770 time to fit residues: 43.0189 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 : 0.461 ------------------------------------------------------------------------------- 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: 6.9990 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 = 0.4034 r_free = 0.4034 target = 0.185382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.172589 restraints weight = 19750.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.151808 restraints weight = 50853.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.148583 restraints weight = 45056.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.147565 restraints weight = 38088.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.147602 restraints weight = 31142.734| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17559 Z= 0.143 Angle : 0.605 9.224 24866 Z= 0.340 Chirality : 0.043 0.312 2809 Planarity : 0.004 0.040 2196 Dihedral : 28.567 173.764 4546 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.13 % Allowed : 11.66 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1346 helix: 1.29 (0.19), residues: 801 sheet: 0.07 (0.69), residues: 64 loop : -1.68 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.024 0.001 TYR I1076 PHE 0.009 0.001 PHE I1152 TRP 0.011 0.001 TRP I 922 HIS 0.003 0.001 HIS I 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (17559) covalent geometry : angle 0.60533 / 0.34 (24866) hydrogen bonds : bond 0.05803 / 4.07 ( 812) hydrogen bonds : angle 3.58622 / 2.57 ( 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 178 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7471 (mtm110) REVERT: C 92 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7869 (mt-10) REVERT: D 86 ARG cc_start: 0.8328 (mpt180) cc_final: 0.7958 (mpt180) REVERT: F 84 MET cc_start: 0.8908 (tpp) cc_final: 0.8594 (tpt) REVERT: H 59 MET cc_start: 0.8547 (tpp) cc_final: 0.8172 (tpp) REVERT: H 62 MET cc_start: 0.9038 (mmm) cc_final: 0.8820 (mmm) REVERT: I 763 GLU cc_start: 0.4772 (tt0) cc_final: 0.4414 (tt0) REVERT: I 792 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7478 (tp) REVERT: I 972 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.4990 (pp) REVERT: I 1011 MET cc_start: 0.7535 (tpp) cc_final: 0.6672 (ttt) outliers start: 25 outliers final: 14 residues processed: 171 average time/residue: 0.1861 time to fit residues: 43.6036 Evaluate side-chains 151 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 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: 0.0470 chunk 73 optimal weight: 6.9990 chunk 85 optimal weight: 0.0020 chunk 80 optimal weight: 0.0970 chunk 23 optimal weight: 0.0980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 overall best weight: 0.1484 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.187765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175761 restraints weight = 19951.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.153660 restraints weight = 48547.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149214 restraints weight = 41965.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.149282 restraints weight = 42456.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.149785 restraints weight = 30655.748| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 17559 Z= 0.123 Angle : 0.557 8.883 24866 Z= 0.317 Chirality : 0.041 0.321 2809 Planarity : 0.004 0.037 2196 Dihedral : 28.368 174.184 4546 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.55 % Allowed : 12.68 % Favored : 84.77 % 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: 1.50 (0.19), residues: 802 sheet: 0.23 (0.68), residues: 64 loop : -1.63 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I1324 TYR 0.018 0.001 TYR I 560 PHE 0.008 0.001 PHE I1316 TRP 0.009 0.001 TRP I 922 HIS 0.004 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.12 (17559) covalent geometry : angle 0.55669 / 0.32 (24866) hydrogen bonds : bond 0.05068 / 3.55 ( 812) hydrogen bonds : angle 3.34474 / 2.40 ( 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 178 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7686 (mtm-85) cc_final: 0.7429 (mtm110) REVERT: D 86 ARG cc_start: 0.8336 (mpt180) cc_final: 0.7969 (mpt180) REVERT: E 112 ILE cc_start: 0.8762 (pt) cc_final: 0.8101 (mt) REVERT: F 84 MET cc_start: 0.8884 (tpp) cc_final: 0.8573 (tpt) REVERT: H 62 MET cc_start: 0.9038 (mmm) cc_final: 0.8828 (mmm) REVERT: I 792 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7533 (tp) REVERT: I 972 LEU cc_start: 0.5773 (OUTLIER) cc_final: 0.4963 (pp) REVERT: I 1105 MET cc_start: 0.7723 (mtt) cc_final: 0.7512 (mtt) outliers start: 30 outliers final: 15 residues processed: 172 average time/residue: 0.1682 time to fit residues: 40.8632 Evaluate side-chains 156 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 58 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 132 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 77 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1062 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.185639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.173315 restraints weight = 19847.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.151476 restraints weight = 49653.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.147638 restraints weight = 41086.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.147910 restraints weight = 40034.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.148273 restraints weight = 27716.063| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17559 Z= 0.132 Angle : 0.566 9.684 24866 Z= 0.316 Chirality : 0.042 0.344 2809 Planarity : 0.004 0.039 2196 Dihedral : 28.464 176.855 4546 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 : 2.21 % Allowed : 14.47 % Favored : 83.32 % 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: 0.57 (0.23), residues: 1346 helix: 1.51 (0.19), residues: 808 sheet: 0.39 (0.69), residues: 64 loop : -1.68 (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 I 560 PHE 0.008 0.001 PHE I1152 TRP 0.010 0.001 TRP I 922 HIS 0.006 0.001 HIS I 868 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (17559) covalent geometry : angle 0.56611 / 0.32 (24866) hydrogen bonds : bond 0.05154 / 3.60 ( 812) hydrogen bonds : angle 3.28438 / 2.35 ( 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 174 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7663 (mtm-85) cc_final: 0.7411 (mtm110) REVERT: B 27 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7493 (mp10) REVERT: D 86 ARG cc_start: 0.8357 (mpt180) cc_final: 0.8017 (mpt180) REVERT: F 84 MET cc_start: 0.8909 (tpp) cc_final: 0.8635 (tpt) REVERT: I 792 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7577 (tp) REVERT: I 801 ARG cc_start: 0.7348 (mmm160) cc_final: 0.6932 (tpm170) REVERT: I 972 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5055 (pp) REVERT: I 1011 MET cc_start: 0.7302 (tpp) cc_final: 0.6707 (ttt) REVERT: I 1366 MET cc_start: 0.5859 (pmm) cc_final: 0.5065 (ptt) outliers start: 26 outliers final: 17 residues processed: 165 average time/residue: 0.1590 time to fit residues: 36.3090 Evaluate side-chains 161 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 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 869 ILE 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 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 1299 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 97 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.183825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.171701 restraints weight = 19807.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.148508 restraints weight = 47090.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.144575 restraints weight = 38482.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.144490 restraints weight = 37065.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.144872 restraints weight = 27778.867| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17559 Z= 0.147 Angle : 0.583 9.067 24866 Z= 0.323 Chirality : 0.042 0.353 2809 Planarity : 0.004 0.044 2196 Dihedral : 28.539 177.976 4546 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.30 % Allowed : 14.64 % Favored : 83.06 % 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: 1.41 (0.19), residues: 808 sheet: 0.39 (0.69), residues: 64 loop : -1.73 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 55 TYR 0.024 0.001 TYR I 820 PHE 0.009 0.001 PHE A 84 TRP 0.010 0.001 TRP I 922 HIS 0.004 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (17559) covalent geometry : angle 0.58322 / 0.32 (24866) hydrogen bonds : bond 0.05263 / 3.68 ( 812) hydrogen bonds : angle 3.31677 / 2.38 ( 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 167 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7645 (mtm-85) cc_final: 0.7403 (mtm110) REVERT: C 92 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: D 86 ARG cc_start: 0.8392 (mpt180) cc_final: 0.8049 (mpt180) REVERT: F 84 MET cc_start: 0.8928 (tpp) cc_final: 0.8657 (tpt) REVERT: G 93 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9301 (mt) REVERT: I 792 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7558 (tp) REVERT: I 801 ARG cc_start: 0.7412 (mmm160) cc_final: 0.6953 (tpm170) REVERT: I 972 LEU cc_start: 0.6165 (OUTLIER) cc_final: 0.5289 (pp) REVERT: I 1011 MET cc_start: 0.7258 (tpp) cc_final: 0.6742 (ttt) REVERT: I 1105 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7599 (mtt) REVERT: I 1366 MET cc_start: 0.6161 (pmm) cc_final: 0.5130 (ptt) outliers start: 27 outliers final: 19 residues processed: 158 average time/residue: 0.1606 time to fit residues: 35.3405 Evaluate side-chains 160 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 96 THR Chi-restraints excluded: chain G residue 93 LEU 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 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1003 LEU Chi-restraints excluded: chain I residue 1105 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 149 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 77 optimal weight: 0.0170 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 110 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 105 optimal weight: 0.0570 chunk 61 optimal weight: 0.5980 chunk 154 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.184612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.172580 restraints weight = 19810.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.151989 restraints weight = 45737.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.148080 restraints weight = 43565.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.148579 restraints weight = 39587.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.148747 restraints weight = 27994.062| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17559 Z= 0.134 Angle : 0.577 14.311 24866 Z= 0.318 Chirality : 0.041 0.348 2809 Planarity : 0.004 0.041 2196 Dihedral : 28.495 178.809 4544 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: 0.50 (0.23), residues: 1346 helix: 1.43 (0.19), residues: 814 sheet: 0.41 (0.69), residues: 64 loop : -1.69 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 99 TYR 0.017 0.001 TYR I 560 PHE 0.009 0.001 PHE I1152 TRP 0.011 0.001 TRP I 922 HIS 0.004 0.001 HIS I1253 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (17559) covalent geometry : angle 0.57735 / 0.32 (24866) hydrogen bonds : bond 0.05117 / 3.57 ( 812) hydrogen bonds : angle 3.27250 / 2.35 ( 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 177 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7471 (mtm180) REVERT: B 27 GLN cc_start: 0.7918 (mp-120) cc_final: 0.7565 (tm-30) REVERT: C 92 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7927 (mp0) REVERT: D 86 ARG cc_start: 0.8381 (mpt180) cc_final: 0.8021 (mpt180) REVERT: F 84 MET cc_start: 0.8890 (tpp) cc_final: 0.8631 (tpt) REVERT: G 58 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8626 (mm) REVERT: G 93 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9280 (mt) REVERT: I 765 LEU cc_start: 0.5657 (pp) cc_final: 0.5026 (mt) REVERT: I 801 ARG cc_start: 0.7246 (mmm160) cc_final: 0.6893 (tpm170) REVERT: I 972 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5232 (pp) REVERT: I 1011 MET cc_start: 0.7273 (tpp) cc_final: 0.6711 (ttt) REVERT: I 1105 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7699 (mtt) REVERT: I 1366 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5150 (ptt) outliers start: 31 outliers final: 19 residues processed: 168 average time/residue: 0.1524 time to fit residues: 36.0247 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 : 0.377 ------------------------------------------------------------------------------- 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 F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain I residue 754 LEU Chi-restraints excluded: chain I residue 781 MET Chi-restraints excluded: chain I residue 807 LEU Chi-restraints excluded: chain I residue 869 ILE 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 1105 MET 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: 0.5980 chunk 65 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1062 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.183209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.171119 restraints weight = 19833.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.149769 restraints weight = 48204.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.145153 restraints weight = 43285.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.145008 restraints weight = 40348.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.144959 restraints weight = 30379.845| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17559 Z= 0.148 Angle : 0.591 12.733 24866 Z= 0.323 Chirality : 0.042 0.361 2809 Planarity : 0.004 0.043 2196 Dihedral : 28.580 179.932 4542 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % 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: 0.46 (0.23), residues: 1346 helix: 1.41 (0.19), residues: 815 sheet: 0.41 (0.70), residues: 64 loop : -1.75 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.017 0.001 TYR I 560 PHE 0.013 0.001 PHE H 70 TRP 0.011 0.001 TRP I 922 HIS 0.009 0.001 HIS I 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (17559) covalent geometry : angle 0.59095 / 0.32 (24866) hydrogen bonds : bond 0.05279 / 3.68 ( 812) hydrogen bonds : angle 3.31395 / 2.38 ( 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 : 0.455 Fit side-chains revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7452 (mtm180) REVERT: B 27 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: C 92 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: D 86 ARG cc_start: 0.8410 (mpt180) cc_final: 0.8064 (mpt180) REVERT: F 84 MET cc_start: 0.8907 (tpp) cc_final: 0.8667 (tpt) REVERT: G 58 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8638 (mm) REVERT: G 104 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7915 (mm110) REVERT: H 59 MET cc_start: 0.8512 (tpp) cc_final: 0.8252 (mmm) REVERT: I 972 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5324 (pp) REVERT: I 1011 MET cc_start: 0.7267 (tpp) cc_final: 0.6718 (ttt) REVERT: I 1105 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7444 (mtt) REVERT: I 1317 MET cc_start: 0.6741 (mmp) cc_final: 0.6229 (mmm) REVERT: I 1366 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.5177 (ptt) outliers start: 32 outliers final: 21 residues processed: 159 average time/residue: 0.1515 time to fit residues: 33.4282 Evaluate side-chains 161 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 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 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 62 ILE 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 1105 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 0.0470 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 98 optimal weight: 0.0570 chunk 125 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.184843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.172856 restraints weight = 19862.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.150487 restraints weight = 47419.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.146358 restraints weight = 40640.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.146459 restraints weight = 37584.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.147271 restraints weight = 26829.652| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17559 Z= 0.126 Angle : 0.578 13.328 24866 Z= 0.316 Chirality : 0.041 0.348 2809 Planarity : 0.004 0.039 2196 Dihedral : 28.503 179.863 4542 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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: 0.58 (0.23), residues: 1346 helix: 1.51 (0.19), residues: 814 sheet: 0.50 (0.70), residues: 64 loop : -1.71 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 801 TYR 0.016 0.001 TYR I 560 PHE 0.011 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 0.00234 / 0.13 (17559) covalent geometry : angle 0.57787 / 0.32 (24866) hydrogen bonds : bond 0.05026 / 3.50 ( 812) hydrogen bonds : angle 3.25544 / 2.33 ( 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 169 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: B 44 LYS cc_start: 0.8565 (tttm) cc_final: 0.8351 (tttm) REVERT: B 92 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8114 (ttp80) REVERT: C 92 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: D 86 ARG cc_start: 0.8347 (mpt180) cc_final: 0.7999 (mpt180) REVERT: F 84 MET cc_start: 0.8855 (tpp) cc_final: 0.8607 (tpt) REVERT: G 58 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8616 (mm) REVERT: G 104 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8028 (mm110) REVERT: H 59 MET cc_start: 0.8428 (tpp) cc_final: 0.8059 (mmm) REVERT: I 972 LEU cc_start: 0.6296 (OUTLIER) cc_final: 0.5426 (pp) REVERT: I 1011 MET cc_start: 0.7326 (tpp) cc_final: 0.6777 (ttt) REVERT: I 1105 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7469 (mtt) REVERT: I 1317 MET cc_start: 0.6775 (mmp) cc_final: 0.6293 (mmm) REVERT: I 1366 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5200 (ptt) outliers start: 32 outliers final: 20 residues processed: 158 average time/residue: 0.1590 time to fit residues: 35.4211 Evaluate side-chains 163 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN 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 971 VAL Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1105 MET 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 1226 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 0.0040 chunk 103 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 44 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1062 HIS I1226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.185123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.172879 restraints weight = 19940.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.150500 restraints weight = 49728.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.147574 restraints weight = 39864.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.146667 restraints weight = 33513.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.146627 restraints weight = 30403.247| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17559 Z= 0.128 Angle : 0.579 12.326 24866 Z= 0.316 Chirality : 0.041 0.349 2809 Planarity : 0.004 0.057 2196 Dihedral : 28.504 179.565 4542 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.55 % Allowed : 15.40 % 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: 0.58 (0.23), residues: 1346 helix: 1.51 (0.19), residues: 814 sheet: 0.50 (0.70), residues: 64 loop : -1.72 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 801 TYR 0.018 0.001 TYR I1076 PHE 0.011 0.001 PHE H 70 TRP 0.011 0.001 TRP I 922 HIS 0.008 0.001 HIS I1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (17559) covalent geometry : angle 0.57866 / 0.32 (24866) hydrogen bonds : bond 0.05033 / 3.51 ( 812) hydrogen bonds : angle 3.24355 / 2.33 ( 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 170 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7747 (mp10) REVERT: B 44 LYS cc_start: 0.8600 (tttm) cc_final: 0.8382 (tttm) REVERT: B 92 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8120 (ttp80) REVERT: C 92 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: D 86 ARG cc_start: 0.8382 (mpt180) cc_final: 0.8041 (mpt180) REVERT: F 84 MET cc_start: 0.8856 (tpp) cc_final: 0.8612 (tpt) REVERT: G 58 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8615 (mm) REVERT: G 104 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8033 (mm110) REVERT: H 59 MET cc_start: 0.8439 (tpp) cc_final: 0.8064 (mmm) REVERT: I 801 ARG cc_start: 0.7567 (mmm160) cc_final: 0.7033 (tpm170) REVERT: I 972 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5467 (pp) REVERT: I 1011 MET cc_start: 0.7308 (tpp) cc_final: 0.6791 (ttt) REVERT: I 1105 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7577 (mtt) REVERT: I 1317 MET cc_start: 0.6866 (mmp) cc_final: 0.6367 (mmm) REVERT: I 1366 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5214 (ptt) outliers start: 30 outliers final: 19 residues processed: 159 average time/residue: 0.1578 time to fit residues: 35.0760 Evaluate side-chains 163 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN 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 971 VAL Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1105 MET 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 1226 GLN 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: 3.9990 chunk 123 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1062 HIS ** I1226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.184078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.172541 restraints weight = 19758.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.149662 restraints weight = 43178.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.146560 restraints weight = 42968.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.146839 restraints weight = 35982.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.147013 restraints weight = 26595.700| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17559 Z= 0.145 Angle : 0.594 11.648 24866 Z= 0.322 Chirality : 0.041 0.361 2809 Planarity : 0.004 0.051 2196 Dihedral : 28.557 179.636 4542 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.21 % Allowed : 15.83 % 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: 0.52 (0.23), residues: 1346 helix: 1.47 (0.19), residues: 814 sheet: 0.48 (0.70), residues: 64 loop : -1.75 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I1325 TYR 0.016 0.001 TYR I1076 PHE 0.012 0.001 PHE H 70 TRP 0.012 0.001 TRP I 922 HIS 0.011 0.001 HIS I 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (17559) covalent geometry : angle 0.59377 / 0.32 (24866) hydrogen bonds : bond 0.05178 / 3.60 ( 812) hydrogen bonds : angle 3.27330 / 2.35 ( 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 159 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.8093 (mp-120) cc_final: 0.7835 (mp10) REVERT: B 44 LYS cc_start: 0.8568 (tttm) cc_final: 0.8350 (tttm) REVERT: B 92 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8129 (ttp80) REVERT: C 92 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: D 86 ARG cc_start: 0.8393 (mpt180) cc_final: 0.8060 (mpt180) REVERT: F 84 MET cc_start: 0.8880 (tpp) cc_final: 0.8655 (tpt) REVERT: G 58 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8657 (mm) REVERT: G 104 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8037 (mm110) REVERT: I 801 ARG cc_start: 0.7572 (mmm160) cc_final: 0.7064 (tpm170) REVERT: I 972 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5411 (pp) REVERT: I 1011 MET cc_start: 0.7349 (tpp) cc_final: 0.6720 (ttt) REVERT: I 1105 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7619 (mtt) REVERT: I 1366 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5191 (ptt) outliers start: 26 outliers final: 18 residues processed: 151 average time/residue: 0.1333 time to fit residues: 28.4374 Evaluate side-chains 157 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 971 VAL Chi-restraints excluded: chain I residue 972 LEU Chi-restraints excluded: chain I residue 992 VAL Chi-restraints excluded: chain I residue 1105 MET 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 89 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 140 optimal weight: 6.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.181494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.168578 restraints weight = 19726.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.146492 restraints weight = 53221.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.143030 restraints weight = 45444.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.142387 restraints weight = 40425.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.142535 restraints weight = 29354.077| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17559 Z= 0.169 Angle : 0.624 11.134 24866 Z= 0.336 Chirality : 0.043 0.382 2809 Planarity : 0.004 0.046 2196 Dihedral : 28.767 179.542 4542 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.38 % Allowed : 15.83 % Favored : 81.79 % 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: 0.37 (0.23), residues: 1346 helix: 1.33 (0.19), residues: 816 sheet: 0.33 (0.69), residues: 64 loop : -1.76 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 71 TYR 0.015 0.001 TYR I 560 PHE 0.013 0.001 PHE H 70 TRP 0.012 0.001 TRP I 922 HIS 0.009 0.001 HIS I 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (17559) covalent geometry : angle 0.62398 / 0.34 (24866) hydrogen bonds : bond 0.05584 / 3.88 ( 812) hydrogen bonds : angle 3.38565 / 2.42 ( 2153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2143.14 seconds wall clock time: 37 minutes 47.70 seconds (2267.70 seconds total)