Starting phenix.real_space_refine on Thu Aug 6 14:48:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cb7_45418/08_2026/9cb7_45418_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cb7_45418/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cb7_45418/08_2026/9cb7_45418_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cb7_45418/08_2026/9cb7_45418_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cb7_45418/08_2026/9cb7_45418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cb7_45418/08_2026/9cb7_45418.map" } 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-2.2rc3-6140/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: 2.88, per 1000 atoms: 0.19 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: 1.07 Conformation dependent library (CDL) restraints added in 391.9 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: 1.88 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: 3.54 Time building geometry restraints manager: 1.49 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: 22617 2.63 - 5.25: 579 5.25 - 7.88: 92 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: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.740 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- 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 : 1.084 13.128 23318 Z= 0.778 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 1.08388 / 0.78 (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 : 0.358 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: 0.8749 (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: 0.8430 (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: 0.9323 (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: 0.7556 (pm20) REVERT: F 65 ASN cc_start: 0.8979 (m-40) cc_final: 0.8705 (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: 0.8624 (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: 0.8452 (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: 0.8637 (t0) REVERT: H 96 GLU cc_start: 0.8027 (pm20) cc_final: 0.7801 (pm20) REVERT: H 109 LEU cc_start: 0.9180 (pp) cc_final: 0.8898 (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 821 GLN cc_start: 0.8349 (pt0) cc_final: 0.7897 (pm20) 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: 0.7243 (mtp) 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: 0.8878 (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: 0.1447 time to fit residues: 53.6404 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 : 0.368 ------------------------------------------------------------------------------- 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: 10.0000 chunk 55 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1359 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.069944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.051580 restraints weight = 119734.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.052665 restraints weight = 73910.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.053368 restraints weight = 54034.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.053819 restraints weight = 44584.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.054085 restraints weight = 39681.862| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1696 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= 0.162 Angle : 0.710 10.620 23318 Z= 0.403 Chirality : 0.047 0.260 2653 Planarity : 0.005 0.063 1944 Dihedral : 31.102 179.569 4491 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.30 % Allowed : 4.78 % Favored : 94.92 % 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: -1.48 (0.23), residues: 1173 helix: -0.42 (0.18), residues: 736 sheet: -0.49 (0.70), residues: 64 loop : -2.03 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 102 TYR 0.037 0.002 TYR H 86 PHE 0.014 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 0.00288 / 0.16 (16325) covalent geometry : angle 0.70979 / 0.40 (23318) hydrogen bonds : bond 0.05497 / 3.61 ( 879) hydrogen bonds : angle 4.12333 / 2.92 ( 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 187 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 184 time to evaluate : 0.421 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: symmetry clash REVERT: B 64 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: B 85 MET cc_start: 0.8635 (tpp) cc_final: 0.8377 (mmm) REVERT: E 81 ASP cc_start: 0.8381 (t70) cc_final: 0.8149 (t70) REVERT: F 37 ARG cc_start: 0.8540 (mtt90) cc_final: 0.8256 (mtm-85) REVERT: H 71 ASP cc_start: 0.9218 (t0) cc_final: 0.8878 (t0) REVERT: H 74 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8389 (tm-30) REVERT: H 87 ASN cc_start: 0.8812 (t0) cc_final: 0.8291 (t0) REVERT: H 116 GLU cc_start: 0.8274 (tp30) cc_final: 0.8012 (tp30) REVERT: Q 712 LYS cc_start: 0.8833 (pttp) cc_final: 0.8604 (tptt) REVERT: Q 816 MET cc_start: 0.6258 (mmt) cc_final: 0.5074 (mpp) REVERT: Q 838 MET cc_start: 0.5436 (ptt) cc_final: 0.5077 (ptp) REVERT: Q 944 LEU cc_start: 0.5908 (mp) cc_final: 0.5590 (mp) REVERT: Q 1005 MET cc_start: 0.7840 (mpp) cc_final: 0.7118 (mtp) REVERT: Q 1321 TYR cc_start: 0.7692 (m-80) cc_final: 0.7466 (m-80) outliers start: 3 outliers final: 1 residues processed: 186 average time/residue: 0.1526 time to fit residues: 39.4770 Evaluate side-chains 132 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 10.0000 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN ** 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 = 0.3752 r_free = 0.3752 target = 0.068827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.050957 restraints weight = 117682.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.052023 restraints weight = 71685.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.052735 restraints weight = 51881.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.053186 restraints weight = 42371.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.053476 restraints weight = 37408.114| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16325 Z= 0.154 Angle : 0.653 10.482 23318 Z= 0.373 Chirality : 0.045 0.271 2653 Planarity : 0.005 0.074 1944 Dihedral : 30.865 179.540 4491 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % 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: -0.89 (0.24), residues: 1173 helix: 0.15 (0.19), residues: 734 sheet: -0.65 (0.70), residues: 64 loop : -1.95 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 33 TYR 0.025 0.002 TYR H 86 PHE 0.012 0.001 PHE Q 813 TRP 0.015 0.001 TRP Q 800 HIS 0.006 0.001 HIS C 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (16325) covalent geometry : angle 0.65296 / 0.37 (23318) hydrogen bonds : bond 0.05057 / 3.36 ( 879) hydrogen bonds : angle 3.84777 / 2.71 ( 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 172 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.454 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: B 64 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: B 85 MET cc_start: 0.8752 (tpp) cc_final: 0.8431 (mmm) REVERT: D 96 GLU cc_start: 0.8689 (mp0) cc_final: 0.8458 (mp0) REVERT: E 81 ASP cc_start: 0.8351 (t70) cc_final: 0.8123 (t70) REVERT: G 37 ARG cc_start: 0.8661 (pmt170) cc_final: 0.8456 (ptt-90) REVERT: H 49 LYS cc_start: 0.9498 (mmmm) cc_final: 0.8950 (mmmm) REVERT: H 71 ASP cc_start: 0.9211 (t0) cc_final: 0.8992 (t0) REVERT: H 74 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8456 (tm-30) REVERT: H 87 ASN cc_start: 0.8870 (t0) cc_final: 0.8370 (t0) REVERT: H 116 GLU cc_start: 0.8245 (tp30) cc_final: 0.7871 (tp30) REVERT: Q 712 LYS cc_start: 0.8797 (pttp) cc_final: 0.8557 (tptt) REVERT: Q 816 MET cc_start: 0.6429 (mmt) cc_final: 0.5338 (mpp) REVERT: Q 838 MET cc_start: 0.5436 (ptt) cc_final: 0.5012 (ptp) REVERT: Q 944 LEU cc_start: 0.5993 (mp) cc_final: 0.5679 (mp) REVERT: Q 1005 MET cc_start: 0.7954 (mpp) cc_final: 0.7251 (mtp) REVERT: Q 1328 MET cc_start: 0.9143 (mmm) cc_final: 0.8737 (mmm) REVERT: Q 1371 LEU cc_start: 0.9234 (tp) cc_final: 0.8954 (tp) outliers start: 1 outliers final: 0 residues processed: 171 average time/residue: 0.1442 time to fit residues: 34.3949 Evaluate side-chains 124 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 0.0970 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 69 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN Q 861 HIS Q 875 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 = 0.3763 r_free = 0.3763 target = 0.069486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.051230 restraints weight = 120206.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.052274 restraints weight = 73761.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.052978 restraints weight = 54004.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.053410 restraints weight = 44598.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.053685 restraints weight = 39687.001| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2335 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= 0.138 Angle : 0.633 10.414 23318 Z= 0.362 Chirality : 0.045 0.274 2653 Planarity : 0.004 0.079 1944 Dihedral : 30.714 179.678 4491 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.24), residues: 1173 helix: 0.44 (0.19), residues: 738 sheet: -0.68 (0.70), residues: 66 loop : -1.87 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 37 TYR 0.029 0.001 TYR F 52 PHE 0.043 0.001 PHE Q1370 TRP 0.044 0.002 TRP Q1361 HIS 0.004 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (16325) covalent geometry : angle 0.63266 / 0.36 (23318) hydrogen bonds : bond 0.04575 / 3.06 ( 879) hydrogen bonds : angle 3.71407 / 2.61 ( 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 181 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.328 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 85 MET cc_start: 0.8700 (tpp) cc_final: 0.8356 (mmm) REVERT: D 96 GLU cc_start: 0.8664 (mp0) cc_final: 0.8423 (mp0) REVERT: E 81 ASP cc_start: 0.8315 (t70) cc_final: 0.8110 (t70) REVERT: E 94 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8468 (mm-30) REVERT: G 89 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8517 (mmm-85) REVERT: G 95 ASN cc_start: 0.9328 (m-40) cc_final: 0.8910 (m-40) REVERT: H 49 LYS cc_start: 0.9550 (mmmm) cc_final: 0.9194 (mmmm) REVERT: H 71 ASP cc_start: 0.9197 (t0) cc_final: 0.8986 (t0) REVERT: H 74 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8378 (tm-30) REVERT: H 82 LYS cc_start: 0.9252 (ptpp) cc_final: 0.9024 (ptpp) REVERT: H 87 ASN cc_start: 0.8825 (t0) cc_final: 0.8301 (t0) REVERT: H 116 GLU cc_start: 0.8207 (tp30) cc_final: 0.7961 (tp30) REVERT: Q 712 LYS cc_start: 0.8725 (pttp) cc_final: 0.8495 (tptt) REVERT: Q 816 MET cc_start: 0.6620 (mmt) cc_final: 0.5557 (mpp) REVERT: Q 838 MET cc_start: 0.5397 (ptt) cc_final: 0.4995 (ptp) REVERT: Q 944 LEU cc_start: 0.5961 (mp) cc_final: 0.5626 (mp) REVERT: Q 1005 MET cc_start: 0.7942 (mpp) cc_final: 0.7319 (mtp) REVERT: Q 1328 MET cc_start: 0.9222 (mmm) cc_final: 0.8908 (mmt) REVERT: Q 1371 LEU cc_start: 0.8933 (tp) cc_final: 0.8705 (tp) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.1342 time to fit residues: 34.0595 Evaluate side-chains 129 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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: 2.9990 chunk 17 optimal weight: 6.9990 chunk 121 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS ** E 68 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 = 0.3738 r_free = 0.3738 target = 0.068257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050302 restraints weight = 122967.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.051389 restraints weight = 75233.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.052069 restraints weight = 54974.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.052496 restraints weight = 45325.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.052756 restraints weight = 40419.612| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16325 Z= 0.154 Angle : 0.635 8.416 23318 Z= 0.364 Chirality : 0.044 0.273 2653 Planarity : 0.005 0.083 1944 Dihedral : 30.601 179.865 4491 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: -0.36 (0.24), residues: 1173 helix: 0.61 (0.19), residues: 737 sheet: -0.46 (0.73), residues: 64 loop : -1.85 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 37 TYR 0.030 0.002 TYR H 86 PHE 0.022 0.002 PHE Q1370 TRP 0.026 0.002 TRP Q 787 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.15 (16325) covalent geometry : angle 0.63527 / 0.36 (23318) hydrogen bonds : bond 0.04772 / 3.17 ( 879) hydrogen bonds : angle 3.64632 / 2.57 ( 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 173 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.448 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: 0.8764 (tpp) cc_final: 0.8338 (mmm) REVERT: D 96 GLU cc_start: 0.8662 (mp0) cc_final: 0.8379 (mp0) REVERT: D 108 GLU cc_start: 0.6798 (pp20) cc_final: 0.6546 (pp20) REVERT: E 81 ASP cc_start: 0.8284 (t70) cc_final: 0.8074 (t70) REVERT: E 94 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8430 (mm-30) REVERT: G 95 ASN cc_start: 0.9305 (m-40) cc_final: 0.9052 (m-40) REVERT: H 49 LYS cc_start: 0.9570 (mmmm) cc_final: 0.9227 (mmmm) REVERT: H 71 ASP cc_start: 0.9250 (t0) cc_final: 0.9046 (t0) REVERT: H 74 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8396 (tm-30) REVERT: H 124 TYR cc_start: 0.9278 (t80) cc_final: 0.9072 (t80) REVERT: Q 712 LYS cc_start: 0.8762 (pttp) cc_final: 0.8515 (tptt) REVERT: Q 816 MET cc_start: 0.6584 (mmt) cc_final: 0.5507 (mpp) REVERT: Q 944 LEU cc_start: 0.5773 (mp) cc_final: 0.5422 (mp) REVERT: Q 1005 MET cc_start: 0.7989 (mpp) cc_final: 0.7381 (mtt) REVERT: Q 1328 MET cc_start: 0.9273 (mmm) cc_final: 0.8918 (mmt) REVERT: Q 1371 LEU cc_start: 0.8901 (tp) cc_final: 0.8551 (tp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1321 time to fit residues: 32.7925 Evaluate side-chains 122 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 3.9990 chunk 13 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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** D 66 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 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 = 0.3706 r_free = 0.3706 target = 0.066987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.049453 restraints weight = 117902.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.050423 restraints weight = 70547.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.051075 restraints weight = 51494.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051498 restraints weight = 42431.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051769 restraints weight = 37706.690| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16325 Z= 0.171 Angle : 0.644 7.956 23318 Z= 0.367 Chirality : 0.045 0.276 2653 Planarity : 0.004 0.057 1944 Dihedral : 30.580 179.274 4491 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.10 % Allowed : 3.96 % Favored : 95.93 % 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: -0.29 (0.24), residues: 1173 helix: 0.70 (0.19), residues: 740 sheet: -0.64 (0.73), residues: 59 loop : -1.88 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 37 TYR 0.032 0.002 TYR F 52 PHE 0.015 0.002 PHE Q1370 TRP 0.013 0.001 TRP Q 800 HIS 0.012 0.001 HIS Q1316 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (16325) covalent geometry : angle 0.64351 / 0.37 (23318) hydrogen bonds : bond 0.05133 / 3.42 ( 879) hydrogen bonds : angle 3.65105 / 2.57 ( 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 163 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8823 (tpp) cc_final: 0.8329 (mmm) REVERT: D 62 MET cc_start: 0.9250 (tpp) cc_final: 0.9041 (tpt) REVERT: D 96 GLU cc_start: 0.8670 (mp0) cc_final: 0.8352 (mp0) REVERT: E 81 ASP cc_start: 0.8344 (t70) cc_final: 0.8140 (t70) REVERT: E 94 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8416 (mm-30) REVERT: G 58 TYR cc_start: 0.9017 (t80) cc_final: 0.8782 (t80) REVERT: H 49 LYS cc_start: 0.9574 (mmmm) cc_final: 0.9242 (mmmm) REVERT: H 74 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8470 (tm-30) REVERT: H 82 LYS cc_start: 0.9243 (ptpp) cc_final: 0.8380 (ptpp) REVERT: Q 712 LYS cc_start: 0.8742 (pttp) cc_final: 0.8463 (tptt) REVERT: Q 816 MET cc_start: 0.6595 (mmt) cc_final: 0.5601 (mpp) REVERT: Q 928 LEU cc_start: 0.8421 (pt) cc_final: 0.8118 (mm) REVERT: Q 1005 MET cc_start: 0.8005 (mpp) cc_final: 0.7393 (mtt) REVERT: Q 1328 MET cc_start: 0.9298 (mmm) cc_final: 0.8920 (mmm) REVERT: Q 1371 LEU cc_start: 0.8938 (tp) cc_final: 0.8667 (tp) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1343 time to fit residues: 30.9116 Evaluate side-chains 113 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 5.9990 chunk 91 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 127 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 0.5980 chunk 122 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1316 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 = 0.3711 r_free = 0.3711 target = 0.067332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.049487 restraints weight = 122667.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050417 restraints weight = 75523.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.051096 restraints weight = 55861.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051519 restraints weight = 46551.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.051722 restraints weight = 41615.365| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16325 Z= 0.142 Angle : 0.626 10.669 23318 Z= 0.354 Chirality : 0.044 0.279 2653 Planarity : 0.004 0.057 1944 Dihedral : 30.511 179.161 4491 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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: -0.20 (0.24), residues: 1173 helix: 0.78 (0.19), residues: 741 sheet: -0.54 (0.72), residues: 64 loop : -1.91 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 93 TYR 0.042 0.002 TYR H 86 PHE 0.012 0.001 PHE Q 813 TRP 0.014 0.001 TRP Q 800 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (16325) covalent geometry : angle 0.62593 / 0.35 (23318) hydrogen bonds : bond 0.04488 / 3.00 ( 879) hydrogen bonds : angle 3.56907 / 2.50 ( 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 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.430 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 85 MET cc_start: 0.8627 (tpp) cc_final: 0.8189 (mmm) REVERT: G 58 TYR cc_start: 0.8982 (t80) cc_final: 0.8754 (t80) REVERT: H 49 LYS cc_start: 0.9495 (mmmm) cc_final: 0.9189 (mmmm) REVERT: H 74 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8211 (tm-30) REVERT: H 75 ARG cc_start: 0.8735 (ttm170) cc_final: 0.8260 (mtm180) REVERT: H 116 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7705 (tm-30) REVERT: Q 712 LYS cc_start: 0.8637 (pttp) cc_final: 0.8366 (tptt) REVERT: Q 816 MET cc_start: 0.6664 (mmt) cc_final: 0.5675 (mpp) REVERT: Q 928 LEU cc_start: 0.8344 (pt) cc_final: 0.8056 (mm) REVERT: Q 1005 MET cc_start: 0.7830 (mpp) cc_final: 0.7324 (mtt) REVERT: Q 1328 MET cc_start: 0.9130 (mmm) cc_final: 0.8726 (mmm) REVERT: Q 1371 LEU cc_start: 0.9037 (tp) cc_final: 0.8639 (tp) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1477 time to fit residues: 32.3966 Evaluate side-chains 113 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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: 0.0970 chunk 16 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 38 optimal weight: 0.0070 chunk 138 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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 ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3712 r_free = 0.3712 target = 0.067430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.049353 restraints weight = 120977.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.050328 restraints weight = 73138.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.051018 restraints weight = 53393.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.051450 restraints weight = 44210.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051700 restraints weight = 39519.687| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16325 Z= 0.138 Angle : 0.622 7.022 23318 Z= 0.353 Chirality : 0.044 0.280 2653 Planarity : 0.004 0.059 1944 Dihedral : 30.420 179.176 4491 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -0.11 (0.24), residues: 1173 helix: 0.82 (0.19), residues: 744 sheet: -0.45 (0.73), residues: 64 loop : -1.84 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 30 TYR 0.036 0.002 TYR H 86 PHE 0.022 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 0.00252 / 0.14 (16325) covalent geometry : angle 0.62187 / 0.35 (23318) hydrogen bonds : bond 0.04323 / 2.90 ( 879) hydrogen bonds : angle 3.50830 / 2.46 ( 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 163 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8825 (tpp) cc_final: 0.8313 (mmm) REVERT: G 58 TYR cc_start: 0.9031 (t80) cc_final: 0.8740 (t80) REVERT: H 49 LYS cc_start: 0.9549 (mmmm) cc_final: 0.9221 (mmmm) REVERT: H 74 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8407 (tm-30) REVERT: H 75 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8425 (mtm180) REVERT: H 82 LYS cc_start: 0.9317 (ptpp) cc_final: 0.8433 (ptpp) REVERT: H 116 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7843 (tm-30) REVERT: Q 712 LYS cc_start: 0.8657 (pttp) cc_final: 0.8373 (tptt) REVERT: Q 816 MET cc_start: 0.6679 (mmt) cc_final: 0.5723 (mpp) REVERT: Q 928 LEU cc_start: 0.8416 (pt) cc_final: 0.8182 (mm) REVERT: Q 1005 MET cc_start: 0.7951 (mpp) cc_final: 0.7402 (mtt) REVERT: Q 1328 MET cc_start: 0.9165 (mmm) cc_final: 0.8702 (mmt) REVERT: Q 1371 LEU cc_start: 0.9029 (tp) cc_final: 0.8814 (tp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1472 time to fit residues: 34.0211 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 : 0.440 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** E 68 GLN ** 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 = 0.3672 r_free = 0.3672 target = 0.065551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047900 restraints weight = 120213.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.048871 restraints weight = 72553.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.049544 restraints weight = 53097.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049944 restraints weight = 43899.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.050195 restraints weight = 39239.187| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16325 Z= 0.187 Angle : 0.670 10.459 23318 Z= 0.376 Chirality : 0.045 0.283 2653 Planarity : 0.005 0.060 1944 Dihedral : 30.479 179.009 4491 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.24), residues: 1173 helix: 0.78 (0.19), residues: 740 sheet: -0.72 (0.72), residues: 60 loop : -1.96 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 93 TYR 0.016 0.002 TYR G 51 PHE 0.018 0.002 PHE Q 813 TRP 0.013 0.001 TRP Q 800 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 (16325) covalent geometry : angle 0.67016 / 0.38 (23318) hydrogen bonds : bond 0.05547 / 3.72 ( 879) hydrogen bonds : angle 3.71391 / 2.62 ( 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 151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8771 (pp20) cc_final: 0.8466 (pp20) REVERT: B 85 MET cc_start: 0.8895 (tpp) cc_final: 0.8068 (mmm) REVERT: B 89 TYR cc_start: 0.8472 (m-80) cc_final: 0.7997 (m-80) REVERT: C 72 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8402 (mtm110) REVERT: E 81 ASP cc_start: 0.8486 (t70) cc_final: 0.8275 (t70) REVERT: G 58 TYR cc_start: 0.9057 (t80) cc_final: 0.8757 (t80) REVERT: H 74 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8441 (tm-30) REVERT: H 75 ARG cc_start: 0.8931 (ttm170) cc_final: 0.8478 (mtm180) REVERT: H 116 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7944 (tm-30) REVERT: Q 816 MET cc_start: 0.6980 (mmt) cc_final: 0.5972 (mpp) REVERT: Q 928 LEU cc_start: 0.8435 (pt) cc_final: 0.8105 (mm) REVERT: Q 1005 MET cc_start: 0.8012 (mpp) cc_final: 0.7429 (mtt) REVERT: Q 1321 TYR cc_start: 0.8524 (m-10) cc_final: 0.8220 (m-10) REVERT: Q 1328 MET cc_start: 0.9234 (mmm) cc_final: 0.8775 (mmt) REVERT: Q 1371 LEU cc_start: 0.9080 (tp) cc_final: 0.8817 (tp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1217 time to fit residues: 26.5529 Evaluate side-chains 118 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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: 0.5980 chunk 86 optimal weight: 40.0000 chunk 139 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.066513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.048823 restraints weight = 117042.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.049867 restraints weight = 70324.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.050525 restraints weight = 51078.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050962 restraints weight = 42175.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.051246 restraints weight = 37506.914| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16325 Z= 0.139 Angle : 0.644 10.079 23318 Z= 0.364 Chirality : 0.044 0.284 2653 Planarity : 0.004 0.060 1944 Dihedral : 30.399 179.212 4491 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.20 % Allowed : 0.30 % Favored : 99.49 % 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 (0.24), residues: 1173 helix: 0.84 (0.19), residues: 747 sheet: -0.70 (0.72), residues: 60 loop : -1.91 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 37 TYR 0.016 0.001 TYR D 43 PHE 0.019 0.001 PHE Q 813 TRP 0.014 0.001 TRP Q 800 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (16325) covalent geometry : angle 0.64414 / 0.36 (23318) hydrogen bonds : bond 0.04359 / 2.94 ( 879) hydrogen bonds : angle 3.61653 / 2.55 ( 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 160 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8808 (pp20) cc_final: 0.8557 (pp20) REVERT: B 85 MET cc_start: 0.8906 (tpp) cc_final: 0.8075 (mmm) REVERT: B 89 TYR cc_start: 0.8479 (m-80) cc_final: 0.8000 (m-80) REVERT: C 72 ARG cc_start: 0.8957 (ttm110) cc_final: 0.8466 (mtm110) REVERT: E 81 ASP cc_start: 0.8399 (t70) cc_final: 0.8155 (t70) REVERT: G 58 TYR cc_start: 0.9036 (t80) cc_final: 0.8732 (t80) REVERT: H 45 TYR cc_start: 0.8586 (t80) cc_final: 0.8094 (t80) REVERT: H 49 LYS cc_start: 0.9569 (mmmm) cc_final: 0.9236 (mmmm) REVERT: H 74 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8424 (tm-30) REVERT: H 75 ARG cc_start: 0.8868 (ttm170) cc_final: 0.8477 (mtm180) REVERT: H 82 LYS cc_start: 0.9294 (ptpt) cc_final: 0.8941 (ptpp) REVERT: H 116 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7890 (tm-30) REVERT: Q 928 LEU cc_start: 0.8487 (pt) cc_final: 0.8189 (mm) REVERT: Q 1005 MET cc_start: 0.7999 (mpp) cc_final: 0.7439 (mtt) REVERT: Q 1328 MET cc_start: 0.9238 (mmm) cc_final: 0.8754 (mmt) REVERT: Q 1432 MET cc_start: 0.9046 (mpp) cc_final: 0.8691 (mpp) outliers start: 2 outliers final: 0 residues processed: 159 average time/residue: 0.1322 time to fit residues: 30.4672 Evaluate side-chains 119 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 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 = 0.3575 r_free = 0.3575 target = 0.061360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.043730 restraints weight = 120785.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.044658 restraints weight = 74018.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.045214 restraints weight = 54853.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.045570 restraints weight = 45898.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.045795 restraints weight = 41332.975| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16325 Z= 0.350 Angle : 0.907 9.589 23318 Z= 0.493 Chirality : 0.055 0.341 2653 Planarity : 0.007 0.073 1944 Dihedral : 30.816 177.599 4491 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.23), residues: 1173 helix: -0.17 (0.18), residues: 760 sheet: -1.51 (0.65), residues: 59 loop : -2.35 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG B 93 TYR 0.030 0.004 TYR F 52 PHE 0.031 0.003 PHE Q1368 TRP 0.014 0.002 TRP Q 787 HIS 0.015 0.003 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.35 (16325) covalent geometry : angle 0.90694 / 0.49 (23318) hydrogen bonds : bond 0.10535 / 7.03 ( 879) hydrogen bonds : angle 4.38957 / 3.09 ( 2266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.18 seconds wall clock time: 49 minutes 27.00 seconds (2967.00 seconds total)