Starting phenix.real_space_refine on Fri Jul 3 19:21:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cb7_45418/07_2026/9cb7_45418_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cb7_45418/07_2026/9cb7_45418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cb7_45418/07_2026/9cb7_45418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cb7_45418/07_2026/9cb7_45418.map" model { file = "/net/cci-nas-00/data/ceres_data/9cb7_45418/07_2026/9cb7_45418_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cb7_45418/07_2026/9cb7_45418_neut.cif" } resolution = 4.04 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 22 5.16 5 C 8824 2.51 5 N 2850 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15448 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2976 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "Q" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3390 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 12, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "Z" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 109 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU B 23 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 23 " occ=0.00 residue: pdb=" N ARG B 24 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 24 " occ=0.00 Time building chain proxies: 3.16, per 1000 atoms: 0.20 Number of scatterers: 15448 At special positions: 0 Unit cell: (116.56, 111.86, 151.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 P 292 15.00 O 3460 8.00 N 2850 7.00 C 8824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 467.2 milliseconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 65.0% alpha, 4.9% beta 143 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.634A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.700A pdb=" N ILE A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.626A pdb=" N ARG B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.247A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 94 removed outlier: 4.287A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.317A pdb=" N VAL C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 removed outlier: 3.629A pdb=" N ASN C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.816A pdb=" N LEU C 117 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 Processing helix chain 'D' and resid 58 through 87 Processing helix chain 'D' and resid 93 through 105 removed outlier: 3.657A pdb=" N ILE D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 127 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.541A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.660A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.728A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 30 removed outlier: 3.718A pdb=" N GLY F 29 " --> pdb=" O ASN F 26 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE F 30 " --> pdb=" O ILE F 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 26 through 30' Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 51 through 77 removed outlier: 3.763A pdb=" N ASN F 65 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR F 72 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.912A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.818A pdb=" N LYS G 21 " --> pdb=" O SER G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.178A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.503A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.930A pdb=" N THR H 51 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.573A pdb=" N ILE H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 126 Processing helix chain 'Q' and resid 709 through 724 removed outlier: 3.845A pdb=" N GLY Q 713 " --> pdb=" O TYR Q 709 " (cutoff:3.500A) Processing helix chain 'Q' and resid 736 through 752 removed outlier: 3.741A pdb=" N GLN Q 740 " --> pdb=" O GLY Q 736 " (cutoff:3.500A) Processing helix chain 'Q' and resid 763 through 777 removed outlier: 4.464A pdb=" N HIS Q 768 " --> pdb=" O ALA Q 764 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN Q 769 " --> pdb=" O SER Q 765 " (cutoff:3.500A) Processing helix chain 'Q' and resid 789 through 800 Processing helix chain 'Q' and resid 819 through 825 Processing helix chain 'Q' and resid 842 through 846 removed outlier: 3.951A pdb=" N ALA Q 845 " --> pdb=" O GLU Q 842 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE Q 846 " --> pdb=" O ALA Q 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 842 through 846' Processing helix chain 'Q' and resid 851 through 859 Processing helix chain 'Q' and resid 878 through 888 Processing helix chain 'Q' and resid 894 through 901 Processing helix chain 'Q' and resid 920 through 928 removed outlier: 3.510A pdb=" N LEU Q 924 " --> pdb=" O GLN Q 920 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS Q 925 " --> pdb=" O LEU Q 921 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET Q 926 " --> pdb=" O ARG Q 922 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE Q 927 " --> pdb=" O ARG Q 923 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU Q 928 " --> pdb=" O LEU Q 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 920 through 928' Processing helix chain 'Q' and resid 957 through 970 removed outlier: 3.929A pdb=" N TYR Q 964 " --> pdb=" O GLN Q 960 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN Q 965 " --> pdb=" O ALA Q 961 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS Q 968 " --> pdb=" O TYR Q 964 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN Q 970 " --> pdb=" O VAL Q 966 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1005 through 1013 removed outlier: 3.542A pdb=" N VAL Q1010 " --> pdb=" O GLN Q1006 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N CYS Q1011 " --> pdb=" O PHE Q1007 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN Q1012 " --> pdb=" O ARG Q1008 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS Q1013 " --> pdb=" O LYS Q1009 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1014 through 1017 removed outlier: 3.773A pdb=" N PHE Q1017 " --> pdb=" O PRO Q1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1014 through 1017' Processing helix chain 'Q' and resid 1290 through 1297 Processing helix chain 'Q' and resid 1298 through 1315 removed outlier: 3.587A pdb=" N ASP Q1305 " --> pdb=" O LEU Q1301 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU Q1306 " --> pdb=" O ARG Q1302 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS Q1310 " --> pdb=" O GLU Q1306 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1324 through 1329 Processing helix chain 'Q' and resid 1330 through 1339 removed outlier: 4.133A pdb=" N TYR Q1337 " --> pdb=" O GLU Q1333 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG Q1338 " --> pdb=" O TYR Q1334 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1350 through 1362 removed outlier: 3.673A pdb=" N ASP Q1356 " --> pdb=" O GLU Q1352 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL Q1358 " --> pdb=" O ARG Q1354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1397 through 1409 removed outlier: 3.914A pdb=" N ALA Q1408 " --> pdb=" O ALA Q1404 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1446 removed outlier: 4.106A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN Q1443 " --> pdb=" O LYS Q1439 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL Q1445 " --> pdb=" O GLN Q1441 " (cutoff:3.500A) Processing helix chain 'Z' and resid 257 through 277 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.153A pdb=" N ARG A 83 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.540A pdb=" N ILE A 119 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.857A pdb=" N ARG C 43 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA5, first strand: chain 'C' and resid 102 through 103 removed outlier: 7.506A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.740A pdb=" N ARG E 83 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 43 through 44 removed outlier: 6.848A pdb=" N ARG G 43 " --> pdb=" O ILE H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'Q' and resid 728 through 730 removed outlier: 3.510A pdb=" N LEU Q 729 " --> pdb=" O LEU Q 867 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR Q 869 " --> pdb=" O LEU Q 729 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET Q 838 " --> pdb=" O LEU Q 866 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU Q 868 " --> pdb=" O MET Q 838 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU Q 840 " --> pdb=" O LEU Q 868 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU Q 759 " --> pdb=" O ILE Q 839 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE Q 758 " --> pdb=" O MET Q 816 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N THR Q 818 " --> pdb=" O PHE Q 758 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL Q 760 " --> pdb=" O THR Q 818 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL Q 817 " --> pdb=" O LEU Q 784 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 948 through 954 removed outlier: 5.785A pdb=" N ILE Q 948 " --> pdb=" O VAL Q1419 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ARG Q1421 " --> pdb=" O ILE Q 948 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE Q 950 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU Q1423 " --> pdb=" O ILE Q 950 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N VAL Q 952 " --> pdb=" O LEU Q1423 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR Q1418 " --> pdb=" O VAL Q1389 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N PHE Q1391 " --> pdb=" O THR Q1418 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR Q1420 " --> pdb=" O PHE Q1391 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU Q1319 " --> pdb=" O ILE Q1390 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL Q1318 " --> pdb=" O PHE Q1370 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU Q1372 " --> pdb=" O VAL Q1318 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE Q1320 " --> pdb=" O LEU Q1372 " (cutoff:3.500A) 511 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 736 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 3.77 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2851 1.33 - 1.45: 5252 1.45 - 1.58: 7599 1.58 - 1.70: 582 1.70 - 1.82: 41 Bond restraints: 16325 Sorted by residual: bond pdb=" C1' DC I 37 " pdb=" N1 DC I 37 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.54e+01 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.38e+01 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.435 1.483 -0.048 1.30e-02 5.92e+03 1.36e+01 bond pdb=" C3' DA I -64 " pdb=" O3' DA I -64 " ideal model delta sigma weight residual 1.435 1.389 0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" C5' DG I 56 " pdb=" C4' DG I 56 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.14e+01 ... (remaining 16320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 22626 2.63 - 5.25: 572 5.25 - 7.88: 90 7.88 - 10.50: 25 10.50 - 13.13: 5 Bond angle restraints: 23318 Sorted by residual: angle pdb=" C VAL G 108 " pdb=" N LEU G 109 " pdb=" CA LEU G 109 " ideal model delta sigma weight residual 120.65 129.59 -8.94 1.36e+00 5.41e-01 4.32e+01 angle pdb=" N GLU B 64 " pdb=" CA GLU B 64 " pdb=" CB GLU B 64 " ideal model delta sigma weight residual 110.30 119.45 -9.15 1.54e+00 4.22e-01 3.53e+01 angle pdb=" N GLU B 75 " pdb=" CA GLU B 75 " pdb=" CB GLU B 75 " ideal model delta sigma weight residual 110.42 119.69 -9.27 1.62e+00 3.81e-01 3.27e+01 angle pdb=" C4' DC I -58 " pdb=" O4' DC I -58 " pdb=" C1' DC I -58 " ideal model delta sigma weight residual 110.10 104.45 5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" N GLU A 97 " pdb=" CA GLU A 97 " pdb=" CB GLU A 97 " ideal model delta sigma weight residual 110.28 118.88 -8.60 1.55e+00 4.16e-01 3.08e+01 ... (remaining 23313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 7494 35.91 - 71.82: 1499 71.82 - 107.74: 48 107.74 - 143.65: 1 143.65 - 179.56: 2 Dihedral angle restraints: 9044 sinusoidal: 5542 harmonic: 3502 Sorted by residual: dihedral pdb=" CA PRO H 106 " pdb=" C PRO H 106 " pdb=" N GLY H 107 " pdb=" CA GLY H 107 " ideal model delta harmonic sigma weight residual -180.00 -149.17 -30.83 0 5.00e+00 4.00e-02 3.80e+01 dihedral pdb=" CA MET Q 822 " pdb=" C MET Q 822 " pdb=" N VAL Q 823 " pdb=" CA VAL Q 823 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ASN B 65 " pdb=" C ASN B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 9041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2236 0.075 - 0.149: 358 0.149 - 0.224: 50 0.224 - 0.299: 6 0.299 - 0.373: 3 Chirality restraints: 2653 Sorted by residual: chirality pdb=" CB ILE Q 873 " pdb=" CA ILE Q 873 " pdb=" CG1 ILE Q 873 " pdb=" CG2 ILE Q 873 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU E 60 " pdb=" CB LEU E 60 " pdb=" CD1 LEU E 60 " pdb=" CD2 LEU E 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB ILE Q 950 " pdb=" CA ILE Q 950 " pdb=" CG1 ILE Q 950 " pdb=" CG2 ILE Q 950 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2650 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 86 " -0.027 2.00e-02 2.50e+03 2.28e-02 1.04e+01 pdb=" CG TYR H 86 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR H 86 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 86 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR H 86 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 86 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 86 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 80 " -0.048 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO G 81 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET Q 833 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C MET Q 833 " 0.050 2.00e-02 2.50e+03 pdb=" O MET Q 833 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS Q 834 " -0.017 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2786 2.77 - 3.31: 13714 3.31 - 3.84: 31187 3.84 - 4.37: 34328 4.37 - 4.90: 49519 Nonbonded interactions: 131534 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLN Q 844 " pdb=" OG1 THR Q 869 " model vdw 2.268 3.040 nonbonded pdb=" O ARG Q1317 " pdb=" OG1 THR Q1388 " model vdw 2.308 3.040 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.330 3.040 nonbonded pdb=" OE2 GLU G 65 " pdb=" OG1 THR H 51 " model vdw 2.337 3.040 ... (remaining 131529 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 25 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 120)) selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' 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=0.00 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: 8.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.460 Find NCS groups from input model: 0.150 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 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 : 0.006 0.070 16325 Z= 0.510 Angle : 1.079 13.128 23318 Z= 0.772 Chirality : 0.058 0.373 2653 Planarity : 0.007 0.073 1944 Dihedral : 27.510 179.562 6770 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.73 (0.21), residues: 1173 helix: -1.58 (0.16), residues: 723 sheet: -0.71 (0.68), residues: 64 loop : -2.14 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 102 TYR 0.057 0.003 TYR H 86 PHE 0.020 0.002 PHE C 26 TRP 0.024 0.003 TRP Q1361 HIS 0.012 0.002 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.51 (16325) covalent geometry : angle 1.07873 / 0.77 (23318) hydrogen bonds : bond 0.13589 / 9.04 ( 879) hydrogen bonds : angle 5.59287 / 3.96 ( 2266) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.9047 (pm20) cc_final: 0.8670 (pm20) REVERT: B 85 MET cc_start: 0.9117 (tpp) cc_final: 0.7753 (mmm) REVERT: B 89 TYR cc_start: 0.8430 (m-80) cc_final: 0.7282 (m-80) REVERT: C 92 ASP cc_start: 0.9137 (p0) cc_final: 0.8748 (p0) REVERT: D 60 LYS cc_start: 0.9220 (ptpp) cc_final: 0.9013 (tttm) REVERT: D 83 LEU cc_start: 0.9593 (tp) cc_final: 0.9377 (tt) REVERT: D 96 GLU cc_start: 0.8854 (mp0) cc_final: 0.8432 (mp0) REVERT: D 108 GLU cc_start: 0.7415 (pp20) cc_final: 0.7152 (pp20) REVERT: E 74 ILE cc_start: 0.9614 (tt) cc_final: 0.9322 (tt) REVERT: F 37 ARG cc_start: 0.8426 (mtt90) cc_final: 0.8098 (mtm-85) REVERT: F 40 ARG cc_start: 0.9186 (mmt180) cc_final: 0.8957 (mmm-85) REVERT: F 53 GLU cc_start: 0.8079 (pm20) cc_final: 0.7557 (pm20) REVERT: F 65 ASN cc_start: 0.8979 (m-40) cc_final: 0.8704 (m-40) REVERT: F 101 PHE cc_start: 0.8621 (m-10) cc_final: 0.8401 (m-80) REVERT: G 58 TYR cc_start: 0.8890 (t80) cc_final: 0.8625 (t80) REVERT: G 69 ASN cc_start: 0.9139 (p0) cc_final: 0.8868 (p0) REVERT: H 55 THR cc_start: 0.9047 (m) cc_final: 0.8842 (m) REVERT: H 71 ASP cc_start: 0.9482 (t0) cc_final: 0.8451 (t0) REVERT: H 75 ARG cc_start: 0.9244 (ttm170) cc_final: 0.8424 (ttm170) REVERT: H 87 ASN cc_start: 0.8939 (t0) cc_final: 0.8612 (t0) REVERT: H 96 GLU cc_start: 0.8027 (pm20) cc_final: 0.7806 (pm20) REVERT: H 109 LEU cc_start: 0.9180 (pp) cc_final: 0.8897 (pp) REVERT: H 111 LYS cc_start: 0.9128 (ptpp) cc_final: 0.8909 (ptpp) REVERT: Q 712 LYS cc_start: 0.8906 (pttp) cc_final: 0.8634 (tptt) REVERT: Q 838 MET cc_start: 0.5417 (ptt) cc_final: 0.5004 (ptp) REVERT: Q 944 LEU cc_start: 0.6189 (mp) cc_final: 0.5903 (mp) REVERT: Q 1005 MET cc_start: 0.8053 (mpp) cc_final: 0.7185 (mtm) REVERT: Q 1322 PHE cc_start: 0.8066 (m-80) cc_final: 0.7069 (m-80) REVERT: Q 1328 MET cc_start: 0.9205 (tpt) cc_final: 0.8879 (mmm) REVERT: Q 1392 TYR cc_start: 0.7857 (t80) cc_final: 0.7475 (t80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1700 time to fit residues: 62.8106 Evaluate side-chains 152 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 875 ASN ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1359 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.069457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.051682 restraints weight = 120871.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.052661 restraints weight = 75144.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.053326 restraints weight = 55700.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.053701 restraints weight = 46445.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.053980 restraints weight = 41767.111| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16325 Z= 0.165 Angle : 0.703 10.293 23318 Z= 0.401 Chirality : 0.047 0.249 2653 Planarity : 0.005 0.072 1944 Dihedral : 31.137 179.057 4491 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.41 % Allowed : 4.57 % Favored : 95.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.23), residues: 1173 helix: -0.36 (0.18), residues: 736 sheet: -0.51 (0.70), residues: 64 loop : -2.01 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 102 TYR 0.040 0.002 TYR H 86 PHE 0.015 0.001 PHE D 68 TRP 0.016 0.001 TRP Q 800 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (16325) covalent geometry : angle 0.70280 / 0.40 (23318) hydrogen bonds : bond 0.05308 / 3.47 ( 879) hydrogen bonds : angle 4.07638 / 2.88 ( 2266) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: B 85 MET cc_start: 0.8615 (tpp) cc_final: 0.8362 (mmm) REVERT: E 81 ASP cc_start: 0.8232 (t70) cc_final: 0.8029 (t70) REVERT: H 71 ASP cc_start: 0.9167 (t0) cc_final: 0.8870 (t0) REVERT: H 74 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8352 (tm-30) REVERT: H 75 ARG cc_start: 0.9045 (ttm170) cc_final: 0.8681 (ttm170) REVERT: H 87 ASN cc_start: 0.8821 (t0) cc_final: 0.8343 (t0) REVERT: H 116 GLU cc_start: 0.8239 (tp30) cc_final: 0.7994 (tp30) REVERT: Q 712 LYS cc_start: 0.8830 (pttp) cc_final: 0.8606 (tptt) REVERT: Q 816 MET cc_start: 0.6292 (mmt) cc_final: 0.5110 (mpp) REVERT: Q 838 MET cc_start: 0.5443 (ptt) cc_final: 0.5072 (ptp) REVERT: Q 944 LEU cc_start: 0.5885 (mp) cc_final: 0.5571 (mp) REVERT: Q 1005 MET cc_start: 0.7890 (mpp) cc_final: 0.7019 (ptp) REVERT: Q 1321 TYR cc_start: 0.7692 (m-80) cc_final: 0.7481 (m-80) outliers start: 4 outliers final: 1 residues processed: 181 average time/residue: 0.1487 time to fit residues: 38.0102 Evaluate side-chains 131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 73 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 66 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 0.0020 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN C 69 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN G 39 ASN ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.071379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.054286 restraints weight = 134383.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.055446 restraints weight = 81725.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.056193 restraints weight = 59349.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.056679 restraints weight = 48698.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.056952 restraints weight = 43303.889| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16325 Z= 0.143 Angle : 0.643 11.360 23318 Z= 0.367 Chirality : 0.045 0.252 2653 Planarity : 0.004 0.066 1944 Dihedral : 30.902 178.510 4491 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % 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: -0.97 (0.24), residues: 1173 helix: 0.06 (0.19), residues: 737 sheet: -0.50 (0.71), residues: 63 loop : -1.98 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 33 TYR 0.025 0.002 TYR H 86 PHE 0.014 0.001 PHE Q1370 TRP 0.015 0.001 TRP Q 800 HIS 0.008 0.001 HIS Q1316 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (16325) covalent geometry : angle 0.64258 / 0.37 (23318) hydrogen bonds : bond 0.04733 / 3.13 ( 879) hydrogen bonds : angle 3.81500 / 2.69 ( 2266) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8804 (pm20) cc_final: 0.8405 (pm20) REVERT: B 85 MET cc_start: 0.8727 (tpp) cc_final: 0.8415 (mmm) REVERT: D 96 GLU cc_start: 0.8630 (mp0) cc_final: 0.8429 (mp0) REVERT: E 81 ASP cc_start: 0.8248 (t70) cc_final: 0.8042 (t70) REVERT: G 95 ASN cc_start: 0.9328 (m-40) cc_final: 0.8892 (m-40) REVERT: H 49 LYS cc_start: 0.9491 (mmmm) cc_final: 0.8944 (mmmm) REVERT: H 71 ASP cc_start: 0.9218 (t0) cc_final: 0.8943 (t0) REVERT: H 74 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8379 (tm-30) REVERT: H 87 ASN cc_start: 0.8829 (t0) cc_final: 0.8376 (t0) REVERT: H 116 GLU cc_start: 0.8096 (tp30) cc_final: 0.7788 (tp30) REVERT: Q 712 LYS cc_start: 0.8810 (pttp) cc_final: 0.8562 (tptt) REVERT: Q 816 MET cc_start: 0.6274 (mmt) cc_final: 0.5216 (mpp) REVERT: Q 838 MET cc_start: 0.5416 (ptt) cc_final: 0.5031 (ptp) REVERT: Q 944 LEU cc_start: 0.5993 (mp) cc_final: 0.5666 (mp) REVERT: Q 1005 MET cc_start: 0.8022 (mpp) cc_final: 0.7131 (ptp) REVERT: Q 1321 TYR cc_start: 0.7810 (m-80) cc_final: 0.7593 (m-80) REVERT: Q 1328 MET cc_start: 0.9092 (mmm) cc_final: 0.8674 (mmm) REVERT: Q 1371 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8919 (tp) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1651 time to fit residues: 41.2907 Evaluate side-chains 126 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 40 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 80 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 861 HIS ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.068540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050813 restraints weight = 117232.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051847 restraints weight = 71151.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.052542 restraints weight = 51815.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.052981 restraints weight = 42534.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.053238 restraints weight = 37628.393| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16325 Z= 0.158 Angle : 0.641 9.769 23318 Z= 0.368 Chirality : 0.044 0.253 2653 Planarity : 0.005 0.081 1944 Dihedral : 30.777 179.131 4491 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1173 helix: 0.46 (0.19), residues: 737 sheet: -0.77 (0.69), residues: 66 loop : -1.85 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 37 TYR 0.026 0.002 TYR F 52 PHE 0.045 0.002 PHE Q1370 TRP 0.062 0.003 TRP Q1361 HIS 0.010 0.001 HIS Q 861 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (16325) covalent geometry : angle 0.64094 / 0.37 (23318) hydrogen bonds : bond 0.04946 / 3.29 ( 879) hydrogen bonds : angle 3.73334 / 2.62 ( 2266) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8821 (tpp) cc_final: 0.8418 (mmm) REVERT: D 96 GLU cc_start: 0.8706 (mp0) cc_final: 0.8433 (mp0) REVERT: E 81 ASP cc_start: 0.8350 (t70) cc_final: 0.8104 (t70) REVERT: E 105 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7890 (tm-30) REVERT: F 96 ARG cc_start: 0.8577 (mtt-85) cc_final: 0.8231 (mtt-85) REVERT: H 49 LYS cc_start: 0.9573 (mmmm) cc_final: 0.9207 (mmmm) REVERT: H 71 ASP cc_start: 0.9277 (t0) cc_final: 0.9062 (t0) REVERT: H 74 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8435 (tm-30) REVERT: Q 712 LYS cc_start: 0.8717 (pttp) cc_final: 0.8489 (tptt) REVERT: Q 816 MET cc_start: 0.6566 (mmt) cc_final: 0.5507 (mpp) REVERT: Q 838 MET cc_start: 0.5410 (ptt) cc_final: 0.4992 (ptp) REVERT: Q 944 LEU cc_start: 0.5778 (mp) cc_final: 0.5448 (mp) REVERT: Q 1005 MET cc_start: 0.7920 (mpp) cc_final: 0.7162 (ptp) REVERT: Q 1321 TYR cc_start: 0.7953 (m-80) cc_final: 0.7700 (m-80) REVERT: Q 1328 MET cc_start: 0.9236 (mmm) cc_final: 0.8753 (mmm) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1504 time to fit residues: 36.5077 Evaluate side-chains 123 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 127 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 9 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.068914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.050743 restraints weight = 120278.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051776 restraints weight = 73005.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.052466 restraints weight = 53299.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.052919 restraints weight = 43976.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.053122 restraints weight = 39171.236| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16325 Z= 0.138 Angle : 0.616 8.905 23318 Z= 0.354 Chirality : 0.044 0.254 2653 Planarity : 0.004 0.061 1944 Dihedral : 30.678 179.510 4491 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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 (0.24), residues: 1173 helix: 0.59 (0.19), residues: 744 sheet: -0.45 (0.74), residues: 64 loop : -1.90 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 37 TYR 0.025 0.002 TYR H 86 PHE 0.019 0.001 PHE Q1370 TRP 0.024 0.002 TRP Q 787 HIS 0.003 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.14 (16325) covalent geometry : angle 0.61613 / 0.35 (23318) hydrogen bonds : bond 0.04381 / 2.92 ( 879) hydrogen bonds : angle 3.68303 / 2.60 ( 2266) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8744 (tpp) cc_final: 0.8330 (mmm) REVERT: C 57 GLU cc_start: 0.8684 (tp30) cc_final: 0.8454 (tp30) REVERT: D 96 GLU cc_start: 0.8627 (mp0) cc_final: 0.8366 (mp0) REVERT: D 108 GLU cc_start: 0.6791 (pp20) cc_final: 0.6543 (pp20) REVERT: E 81 ASP cc_start: 0.8255 (t70) cc_final: 0.8046 (t70) REVERT: F 101 PHE cc_start: 0.9016 (m-80) cc_final: 0.8803 (m-80) REVERT: G 95 ASN cc_start: 0.9238 (m-40) cc_final: 0.8862 (m-40) REVERT: H 49 LYS cc_start: 0.9566 (mmmm) cc_final: 0.9231 (mmmm) REVERT: H 74 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8374 (tm-30) REVERT: H 75 ARG cc_start: 0.9001 (ttm170) cc_final: 0.8335 (mtm180) REVERT: Q 712 LYS cc_start: 0.8755 (pttp) cc_final: 0.8506 (tptt) REVERT: Q 816 MET cc_start: 0.6564 (mmt) cc_final: 0.5463 (mpp) REVERT: Q 838 MET cc_start: 0.5491 (ptt) cc_final: 0.5060 (ptp) REVERT: Q 928 LEU cc_start: 0.8375 (pt) cc_final: 0.8043 (mt) REVERT: Q 944 LEU cc_start: 0.5756 (mp) cc_final: 0.5395 (mp) REVERT: Q 1005 MET cc_start: 0.7910 (mpp) cc_final: 0.7183 (ptp) REVERT: Q 1321 TYR cc_start: 0.7974 (m-80) cc_final: 0.7686 (m-80) REVERT: Q 1328 MET cc_start: 0.9248 (mmm) cc_final: 0.8922 (mmt) REVERT: Q 1371 LEU cc_start: 0.8902 (tp) cc_final: 0.8470 (tp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.1430 time to fit residues: 34.5411 Evaluate side-chains 121 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 55 optimal weight: 0.0470 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 814 HIS ** Q1323 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 = 0.3745 r_free = 0.3745 target = 0.068630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.050750 restraints weight = 116283.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.051831 restraints weight = 70418.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.052543 restraints weight = 50967.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.053007 restraints weight = 41685.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.053308 restraints weight = 36786.014| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16325 Z= 0.133 Angle : 0.613 7.599 23318 Z= 0.351 Chirality : 0.043 0.255 2653 Planarity : 0.004 0.088 1944 Dihedral : 30.574 179.671 4491 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.24), residues: 1173 helix: 0.71 (0.19), residues: 741 sheet: -0.59 (0.73), residues: 65 loop : -1.84 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 37 TYR 0.023 0.001 TYR H 86 PHE 0.014 0.001 PHE Q1370 TRP 0.014 0.001 TRP Q 800 HIS 0.009 0.001 HIS Q1316 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (16325) covalent geometry : angle 0.61272 / 0.35 (23318) hydrogen bonds : bond 0.04311 / 2.86 ( 879) hydrogen bonds : angle 3.55666 / 2.49 ( 2266) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8791 (tpp) cc_final: 0.8293 (mmm) REVERT: C 57 GLU cc_start: 0.8718 (tp30) cc_final: 0.8444 (tp30) REVERT: D 79 GLU cc_start: 0.8269 (tp30) cc_final: 0.8064 (tp30) REVERT: D 96 GLU cc_start: 0.8657 (mp0) cc_final: 0.8305 (mp0) REVERT: E 81 ASP cc_start: 0.8306 (t70) cc_final: 0.8074 (t70) REVERT: G 95 ASN cc_start: 0.9265 (m-40) cc_final: 0.8845 (m-40) REVERT: H 49 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9240 (mmmm) REVERT: H 74 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8446 (tm-30) REVERT: H 75 ARG cc_start: 0.9001 (ttm170) cc_final: 0.8558 (mtm180) REVERT: Q 712 LYS cc_start: 0.8690 (pttp) cc_final: 0.8437 (tptt) REVERT: Q 816 MET cc_start: 0.6473 (mmt) cc_final: 0.5622 (mpp) REVERT: Q 1005 MET cc_start: 0.7952 (mpp) cc_final: 0.7378 (mtp) REVERT: Q 1321 TYR cc_start: 0.8091 (m-80) cc_final: 0.7750 (m-80) REVERT: Q 1328 MET cc_start: 0.9231 (mmm) cc_final: 0.8860 (mmm) REVERT: Q 1371 LEU cc_start: 0.8817 (tp) cc_final: 0.8252 (tp) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.1422 time to fit residues: 34.0999 Evaluate side-chains 124 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 3 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 123 optimal weight: 0.0770 chunk 122 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 42 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.068511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050315 restraints weight = 120846.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.051320 restraints weight = 73520.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.051999 restraints weight = 53977.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.052465 restraints weight = 44912.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052714 restraints weight = 39954.142| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16325 Z= 0.135 Angle : 0.606 10.123 23318 Z= 0.347 Chirality : 0.043 0.255 2653 Planarity : 0.004 0.066 1944 Dihedral : 30.505 179.837 4491 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.10 % Allowed : 2.44 % Favored : 97.46 % 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 (0.25), residues: 1173 helix: 0.79 (0.19), residues: 742 sheet: -0.55 (0.72), residues: 64 loop : -1.80 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 37 TYR 0.022 0.001 TYR F 52 PHE 0.012 0.001 PHE Q 813 TRP 0.015 0.001 TRP Q 800 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.13 (16325) covalent geometry : angle 0.60572 / 0.35 (23318) hydrogen bonds : bond 0.04287 / 2.84 ( 879) hydrogen bonds : angle 3.53107 / 2.48 ( 2266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8822 (tpp) cc_final: 0.8347 (mmm) REVERT: C 57 GLU cc_start: 0.8719 (tp30) cc_final: 0.8460 (tp30) REVERT: D 96 GLU cc_start: 0.8606 (mp0) cc_final: 0.8328 (mp0) REVERT: E 81 ASP cc_start: 0.8335 (t70) cc_final: 0.8073 (t70) REVERT: E 94 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8135 (mm-30) REVERT: H 49 LYS cc_start: 0.9586 (mmmm) cc_final: 0.9246 (mmmm) REVERT: H 71 ASP cc_start: 0.9117 (t0) cc_final: 0.8442 (t0) REVERT: H 74 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8457 (tm-30) REVERT: H 75 ARG cc_start: 0.8884 (ttm170) cc_final: 0.8266 (ttm170) REVERT: Q 712 LYS cc_start: 0.8655 (pttp) cc_final: 0.8393 (tptt) REVERT: Q 816 MET cc_start: 0.6570 (mmt) cc_final: 0.5749 (mpp) REVERT: Q 1005 MET cc_start: 0.7935 (mpp) cc_final: 0.7366 (mtt) REVERT: Q 1321 TYR cc_start: 0.8091 (m-80) cc_final: 0.7749 (m-80) REVERT: Q 1328 MET cc_start: 0.9198 (mmm) cc_final: 0.8738 (mmt) REVERT: Q 1371 LEU cc_start: 0.8875 (tp) cc_final: 0.8664 (tp) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1485 time to fit residues: 34.9951 Evaluate side-chains 124 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 50 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 38 optimal weight: 0.0470 chunk 138 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.068472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.050283 restraints weight = 121624.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.051308 restraints weight = 73341.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.052017 restraints weight = 53599.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.052464 restraints weight = 44385.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.052714 restraints weight = 39692.713| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16325 Z= 0.132 Angle : 0.610 7.169 23318 Z= 0.348 Chirality : 0.043 0.256 2653 Planarity : 0.004 0.058 1944 Dihedral : 30.448 179.810 4491 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.09 (0.25), residues: 1173 helix: 0.83 (0.19), residues: 740 sheet: -0.56 (0.71), residues: 64 loop : -1.74 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 30 TYR 0.019 0.001 TYR H 86 PHE 0.020 0.001 PHE Q 813 TRP 0.015 0.001 TRP Q 800 HIS 0.003 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (16325) covalent geometry : angle 0.61021 / 0.35 (23318) hydrogen bonds : bond 0.04167 / 2.77 ( 879) hydrogen bonds : angle 3.56854 / 2.50 ( 2266) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8831 (tpp) cc_final: 0.8334 (mmm) REVERT: C 57 GLU cc_start: 0.8752 (tp30) cc_final: 0.8486 (tp30) REVERT: D 96 GLU cc_start: 0.8621 (mp0) cc_final: 0.8353 (mp0) REVERT: D 108 GLU cc_start: 0.6676 (pp20) cc_final: 0.6242 (pp20) REVERT: E 81 ASP cc_start: 0.8343 (t70) cc_final: 0.8068 (t70) REVERT: E 94 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8158 (mm-30) REVERT: H 49 LYS cc_start: 0.9570 (mmmm) cc_final: 0.9266 (mmmm) REVERT: H 71 ASP cc_start: 0.9124 (t0) cc_final: 0.8457 (t0) REVERT: H 74 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8398 (tm-30) REVERT: H 75 ARG cc_start: 0.8883 (ttm170) cc_final: 0.8241 (ttm170) REVERT: Q 712 LYS cc_start: 0.8656 (pttp) cc_final: 0.8374 (tptt) REVERT: Q 816 MET cc_start: 0.6703 (mmt) cc_final: 0.5897 (mpp) REVERT: Q 1005 MET cc_start: 0.7930 (mpp) cc_final: 0.7379 (mtt) REVERT: Q 1321 TYR cc_start: 0.8095 (m-80) cc_final: 0.7731 (m-80) REVERT: Q 1328 MET cc_start: 0.9172 (mmm) cc_final: 0.8773 (mmt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1413 time to fit residues: 32.4057 Evaluate side-chains 127 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.064490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.046337 restraints weight = 122048.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.047354 restraints weight = 74830.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.048010 restraints weight = 55311.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.048400 restraints weight = 46091.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048519 restraints weight = 41364.816| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 16325 Z= 0.232 Angle : 0.743 11.277 23318 Z= 0.412 Chirality : 0.047 0.268 2653 Planarity : 0.005 0.059 1944 Dihedral : 30.676 178.925 4491 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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 (0.24), residues: 1173 helix: 0.50 (0.19), residues: 747 sheet: -1.12 (0.69), residues: 60 loop : -1.89 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 37 TYR 0.039 0.003 TYR H 86 PHE 0.026 0.002 PHE Q1368 TRP 0.012 0.002 TRP Q 800 HIS 0.010 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (16325) covalent geometry : angle 0.74322 / 0.41 (23318) hydrogen bonds : bond 0.07728 / 5.14 ( 879) hydrogen bonds : angle 3.94336 / 2.76 ( 2266) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8886 (tpp) cc_final: 0.8353 (mmm) REVERT: B 89 TYR cc_start: 0.8497 (m-80) cc_final: 0.8200 (m-80) REVERT: C 57 GLU cc_start: 0.8727 (tp30) cc_final: 0.8434 (tp30) REVERT: D 96 GLU cc_start: 0.8697 (mp0) cc_final: 0.8469 (mp0) REVERT: E 81 ASP cc_start: 0.8433 (t70) cc_final: 0.8232 (t70) REVERT: H 45 TYR cc_start: 0.8369 (t80) cc_final: 0.8011 (t80) REVERT: H 49 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9250 (mmmm) REVERT: H 62 MET cc_start: 0.8643 (tpp) cc_final: 0.8391 (tpp) REVERT: H 74 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8496 (tm-30) REVERT: H 111 LYS cc_start: 0.9340 (ptmm) cc_final: 0.9114 (pttm) REVERT: H 123 LYS cc_start: 0.9373 (tttm) cc_final: 0.9033 (tttm) REVERT: Q 816 MET cc_start: 0.6901 (mmt) cc_final: 0.6035 (mpp) REVERT: Q 1005 MET cc_start: 0.8015 (mpp) cc_final: 0.7411 (mtt) REVERT: Q 1321 TYR cc_start: 0.8414 (m-80) cc_final: 0.7910 (m-80) REVERT: Q 1328 MET cc_start: 0.9210 (mmm) cc_final: 0.8808 (mmt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1511 time to fit residues: 31.9175 Evaluate side-chains 115 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 65 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 139 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 126 optimal weight: 0.0170 chunk 87 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN E 68 GLN ** F 28 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 = 0.3679 r_free = 0.3679 target = 0.066095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.048065 restraints weight = 122591.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.049118 restraints weight = 74357.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.049811 restraints weight = 54500.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.050248 restraints weight = 45026.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.050438 restraints weight = 40233.530| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16325 Z= 0.141 Angle : 0.641 9.440 23318 Z= 0.362 Chirality : 0.044 0.268 2653 Planarity : 0.004 0.057 1944 Dihedral : 30.564 179.791 4491 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.10 % Allowed : 0.61 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.24), residues: 1173 helix: 0.79 (0.19), residues: 745 sheet: -0.99 (0.68), residues: 60 loop : -1.82 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 37 TYR 0.031 0.002 TYR F 52 PHE 0.020 0.002 PHE Q 813 TRP 0.013 0.001 TRP Q 787 HIS 0.013 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (16325) covalent geometry : angle 0.64117 / 0.36 (23318) hydrogen bonds : bond 0.04623 / 3.08 ( 879) hydrogen bonds : angle 3.68167 / 2.57 ( 2266) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8795 (pp20) cc_final: 0.8592 (pp20) REVERT: B 85 MET cc_start: 0.8843 (tpp) cc_final: 0.8071 (mmm) REVERT: B 89 TYR cc_start: 0.8517 (m-80) cc_final: 0.8023 (m-80) REVERT: C 72 ARG cc_start: 0.8959 (ttm110) cc_final: 0.8470 (mtm110) REVERT: E 81 ASP cc_start: 0.8397 (t70) cc_final: 0.8195 (t70) REVERT: G 58 TYR cc_start: 0.9043 (t80) cc_final: 0.8738 (t80) REVERT: H 74 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8396 (tm-30) REVERT: H 75 ARG cc_start: 0.8807 (ttm170) cc_final: 0.8366 (mtm180) REVERT: H 111 LYS cc_start: 0.9312 (ptmm) cc_final: 0.9105 (pttm) REVERT: H 123 LYS cc_start: 0.9335 (tttm) cc_final: 0.9028 (tttm) REVERT: Q 816 MET cc_start: 0.6948 (mmt) cc_final: 0.6023 (mpp) REVERT: Q 1005 MET cc_start: 0.8023 (mpp) cc_final: 0.7448 (mtt) REVERT: Q 1321 TYR cc_start: 0.8325 (m-80) cc_final: 0.7834 (m-80) REVERT: Q 1328 MET cc_start: 0.9215 (mmm) cc_final: 0.8790 (mmt) REVERT: Q 1432 MET cc_start: 0.9129 (mpp) cc_final: 0.8754 (mpp) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.1559 time to fit residues: 33.2324 Evaluate side-chains 117 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 32 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.065251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.047677 restraints weight = 117292.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.048676 restraints weight = 70381.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.049354 restraints weight = 51341.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.049774 restraints weight = 42366.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.050039 restraints weight = 37564.312| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16325 Z= 0.166 Angle : 0.660 9.930 23318 Z= 0.371 Chirality : 0.044 0.266 2653 Planarity : 0.004 0.055 1944 Dihedral : 30.497 179.916 4491 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.24), residues: 1173 helix: 0.81 (0.19), residues: 746 sheet: -1.12 (0.67), residues: 60 loop : -1.84 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 37 TYR 0.018 0.002 TYR H 86 PHE 0.019 0.002 PHE Q 813 TRP 0.012 0.001 TRP Q 800 HIS 0.012 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (16325) covalent geometry : angle 0.65966 / 0.37 (23318) hydrogen bonds : bond 0.05077 / 3.36 ( 879) hydrogen bonds : angle 3.71798 / 2.60 ( 2266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3207.27 seconds wall clock time: 56 minutes 6.74 seconds (3366.74 seconds total)