Starting phenix.real_space_refine on Thu Sep 18 09:40:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cb7_45418/09_2025/9cb7_45418_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cb7_45418/09_2025/9cb7_45418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cb7_45418/09_2025/9cb7_45418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cb7_45418/09_2025/9cb7_45418.map" model { file = "/net/cci-nas-00/data/ceres_data/9cb7_45418/09_2025/9cb7_45418_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cb7_45418/09_2025/9cb7_45418_neut.cif" } resolution = 4.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 22 5.16 5 C 8824 2.51 5 N 2850 2.21 5 O 3460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15448 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 620 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2976 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "Q" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3390 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 12, 'TRANS': 412} Chain breaks: 4 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 12, 'ASN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "Z" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 109 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU B 23 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 23 " occ=0.00 residue: pdb=" N ARG B 24 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 24 " occ=0.00 Time building chain proxies: 3.69, per 1000 atoms: 0.24 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: 1.26 Conformation dependent library (CDL) restraints added in 493.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 11 sheets defined 65.0% alpha, 4.9% beta 143 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 2.60 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: 3.93 Time building geometry restraints manager: 1.75 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=" CD GLU B 64 " pdb=" OE1 GLU B 64 " ideal model delta sigma weight residual 1.249 1.210 0.039 1.90e-02 2.77e+03 4.26e+00 bond pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.16e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.483 -0.061 3.00e-02 1.11e+03 4.12e+00 bond pdb=" CB ASN C 115 " pdb=" CG ASN C 115 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 4.05e+00 bond pdb=" CG1 ILE H 104 " pdb=" CD1 ILE H 104 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.21e+00 ... (remaining 16320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 22760 2.63 - 5.25: 439 5.25 - 7.88: 89 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=" 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 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+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: 2299 0.075 - 0.149: 298 0.149 - 0.224: 47 0.224 - 0.299: 6 0.299 - 0.373: 3 Chirality restraints: 2653 Sorted by residual: chirality pdb=" CB ILE Q 873 " pdb=" CA ILE Q 873 " pdb=" CG1 ILE Q 873 " pdb=" CG2 ILE Q 873 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CG LEU E 60 " pdb=" CB LEU E 60 " pdb=" CD1 LEU E 60 " pdb=" CD2 LEU E 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB ILE Q 950 " pdb=" CA ILE Q 950 " pdb=" CG1 ILE Q 950 " pdb=" CG2 ILE Q 950 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 2650 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 86 " -0.027 2.00e-02 2.50e+03 2.28e-02 1.04e+01 pdb=" CG TYR H 86 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR H 86 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR H 86 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR H 86 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR H 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 86 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR H 86 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 80 " -0.048 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO G 81 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET Q 833 " -0.014 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C MET Q 833 " 0.050 2.00e-02 2.50e+03 pdb=" O MET Q 833 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS Q 834 " -0.017 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2786 2.77 - 3.31: 13714 3.31 - 3.84: 31187 3.84 - 4.37: 34328 4.37 - 4.90: 49519 Nonbonded interactions: 131534 Sorted by model distance: nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLN Q 844 " pdb=" OG1 THR Q 869 " model vdw 2.268 3.040 nonbonded pdb=" O ARG Q1317 " pdb=" OG1 THR Q1388 " model vdw 2.308 3.040 nonbonded pdb=" O LEU A 103 " pdb=" OG1 THR A 107 " model vdw 2.330 3.040 nonbonded pdb=" OE2 GLU G 65 " pdb=" OG1 THR H 51 " model vdw 2.337 3.040 ... (remaining 131529 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 25 through 91 or (resid 92 and (name N or name CA or name \ C or name O or name CB )) or resid 93 through 103)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 62 or (resid 63 and (name N or name CA or name \ C or name O or name CB )) or resid 64 through 87 or (resid 88 and (name N or nam \ e CA or name C or name O or name CB )) or resid 89 through 120)) selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.470 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- 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 : 0.005 0.070 16325 Z= 0.241 Angle : 0.988 13.128 23318 Z= 0.543 Chirality : 0.055 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 aren 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 covalent geometry : bond 0.00516 (16325) covalent geometry : angle 0.98773 (23318) hydrogen bonds : bond 0.13589 ( 879) hydrogen bonds : angle 5.59287 ( 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 : 0.485 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: 0.8669 (pm20) REVERT: B 85 MET cc_start: 0.9117 (tpp) cc_final: 0.7753 (mmm) REVERT: B 89 TYR cc_start: 0.8430 (m-80) cc_final: 0.7282 (m-80) REVERT: C 92 ASP cc_start: 0.9137 (p0) cc_final: 0.8748 (p0) REVERT: D 60 LYS cc_start: 0.9220 (ptpp) cc_final: 0.9013 (tttm) REVERT: D 83 LEU cc_start: 0.9593 (tp) cc_final: 0.9377 (tt) REVERT: D 96 GLU cc_start: 0.8854 (mp0) cc_final: 0.8432 (mp0) REVERT: D 108 GLU cc_start: 0.7415 (pp20) cc_final: 0.7152 (pp20) REVERT: E 74 ILE cc_start: 0.9614 (tt) cc_final: 0.9322 (tt) REVERT: F 37 ARG cc_start: 0.8426 (mtt90) cc_final: 0.8098 (mtm-85) REVERT: F 40 ARG cc_start: 0.9186 (mmt180) cc_final: 0.8957 (mmm-85) REVERT: F 53 GLU cc_start: 0.8079 (pm20) cc_final: 0.7557 (pm20) REVERT: F 65 ASN cc_start: 0.8979 (m-40) cc_final: 0.8704 (m-40) REVERT: F 101 PHE cc_start: 0.8621 (m-10) cc_final: 0.8401 (m-80) REVERT: G 58 TYR cc_start: 0.8890 (t80) cc_final: 0.8625 (t80) REVERT: G 69 ASN cc_start: 0.9139 (p0) cc_final: 0.8868 (p0) REVERT: H 55 THR cc_start: 0.9047 (m) cc_final: 0.8842 (m) REVERT: H 71 ASP cc_start: 0.9482 (t0) cc_final: 0.8451 (t0) REVERT: H 75 ARG cc_start: 0.9244 (ttm170) cc_final: 0.8424 (ttm170) REVERT: H 87 ASN cc_start: 0.8939 (t0) cc_final: 0.8612 (t0) REVERT: H 96 GLU cc_start: 0.8027 (pm20) cc_final: 0.7806 (pm20) REVERT: H 109 LEU cc_start: 0.9180 (pp) cc_final: 0.8897 (pp) REVERT: H 111 LYS cc_start: 0.9128 (ptpp) cc_final: 0.8909 (ptpp) REVERT: Q 712 LYS cc_start: 0.8906 (pttp) cc_final: 0.8634 (tptt) REVERT: Q 838 MET cc_start: 0.5417 (ptt) cc_final: 0.5004 (ptp) REVERT: Q 944 LEU cc_start: 0.6189 (mp) cc_final: 0.5903 (mp) REVERT: Q 1005 MET cc_start: 0.8053 (mpp) cc_final: 0.7185 (mtm) REVERT: Q 1322 PHE cc_start: 0.8066 (m-80) cc_final: 0.7069 (m-80) REVERT: Q 1328 MET cc_start: 0.9205 (tpt) cc_final: 0.8879 (mmm) REVERT: Q 1392 TYR cc_start: 0.7857 (t80) cc_final: 0.7475 (t80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1677 time to fit residues: 61.4711 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 : 0.444 ------------------------------------------------------------------------------- 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: 7.9990 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: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN ** Q 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 861 HIS ** Q 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 875 ASN ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1359 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.068887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.050736 restraints weight = 119473.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051758 restraints weight = 73360.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.052466 restraints weight = 54046.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.052912 restraints weight = 44756.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.053136 restraints weight = 39753.428| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16325 Z= 0.160 Angle : 0.624 10.794 23318 Z= 0.357 Chirality : 0.038 0.176 2653 Planarity : 0.005 0.060 1944 Dihedral : 30.421 176.879 4491 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.10 % Allowed : 6.30 % Favored : 93.60 % 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 aren not related in a simple way. whole: -1.11 (0.23), residues: 1173 helix: -0.10 (0.19), residues: 742 sheet: -0.38 (0.69), residues: 64 loop : -1.99 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 37 TYR 0.036 0.002 TYR H 86 PHE 0.013 0.001 PHE D 68 TRP 0.014 0.001 TRP Q 800 HIS 0.006 0.001 HIS Q 768 Details of bonding type rmsd covalent geometry : bond 0.00338 (16325) covalent geometry : angle 0.62351 (23318) hydrogen bonds : bond 0.04316 ( 879) hydrogen bonds : angle 3.74711 ( 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 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.366 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 85 MET cc_start: 0.8747 (tpp) cc_final: 0.8395 (mmm) REVERT: E 81 ASP cc_start: 0.8271 (t70) cc_final: 0.8019 (t70) REVERT: F 101 PHE cc_start: 0.8776 (m-10) cc_final: 0.8522 (m-80) REVERT: G 95 ASN cc_start: 0.9337 (m-40) cc_final: 0.9071 (m-40) REVERT: H 49 LYS cc_start: 0.9550 (mmmm) cc_final: 0.9048 (mmmm) REVERT: H 71 ASP cc_start: 0.9245 (t0) cc_final: 0.9014 (t0) REVERT: H 74 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8307 (tm-30) REVERT: H 87 ASN cc_start: 0.8734 (t0) cc_final: 0.8250 (t0) REVERT: H 116 GLU cc_start: 0.8334 (tp30) cc_final: 0.7193 (tp30) REVERT: H 119 ARG cc_start: 0.8842 (ttp80) cc_final: 0.8549 (ttp80) REVERT: Q 712 LYS cc_start: 0.8730 (pttp) cc_final: 0.8481 (tptt) REVERT: Q 838 MET cc_start: 0.5489 (ptt) cc_final: 0.5156 (ptp) REVERT: Q 944 LEU cc_start: 0.5965 (mp) cc_final: 0.5596 (mp) REVERT: Q 1005 MET cc_start: 0.7967 (mpp) cc_final: 0.7141 (ptp) REVERT: Q 1321 TYR cc_start: 0.7985 (m-80) cc_final: 0.7637 (m-80) REVERT: Q 1322 PHE cc_start: 0.8099 (m-80) cc_final: 0.7855 (m-80) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.1541 time to fit residues: 39.9681 Evaluate side-chains 127 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.0980 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS C 39 ASN C 69 ASN D 66 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 740 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.068623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050806 restraints weight = 116826.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.051818 restraints weight = 69833.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.052504 restraints weight = 51058.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.052883 restraints weight = 42161.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.053194 restraints weight = 37817.981| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16325 Z= 0.144 Angle : 0.586 8.985 23318 Z= 0.336 Chirality : 0.037 0.184 2653 Planarity : 0.004 0.055 1944 Dihedral : 30.153 177.374 4491 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 5.08 % 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 aren not related in a simple way. whole: -0.37 (0.24), residues: 1173 helix: 0.54 (0.19), residues: 741 sheet: -0.23 (0.69), residues: 65 loop : -1.79 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 33 TYR 0.023 0.001 TYR H 86 PHE 0.012 0.001 PHE Q1370 TRP 0.015 0.001 TRP Q 800 HIS 0.006 0.001 HIS Q1316 Details of bonding type rmsd covalent geometry : bond 0.00304 (16325) covalent geometry : angle 0.58640 (23318) hydrogen bonds : bond 0.03818 ( 879) hydrogen bonds : angle 3.48538 ( 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 185 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8816 (pp20) cc_final: 0.8523 (pp20) REVERT: B 85 MET cc_start: 0.8894 (tpp) cc_final: 0.8444 (mmm) REVERT: D 96 GLU cc_start: 0.8734 (mp0) cc_final: 0.8493 (mp0) REVERT: D 108 GLU cc_start: 0.6848 (pp20) cc_final: 0.6592 (pp20) REVERT: E 81 ASP cc_start: 0.8403 (t70) cc_final: 0.8138 (t70) REVERT: F 101 PHE cc_start: 0.8756 (m-10) cc_final: 0.8450 (m-80) REVERT: G 95 ASN cc_start: 0.9326 (m-40) cc_final: 0.8954 (m-40) REVERT: H 49 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9275 (mmmm) REVERT: H 74 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8392 (tm-30) REVERT: H 75 ARG cc_start: 0.9032 (ttm170) cc_final: 0.8373 (mtm180) REVERT: H 86 TYR cc_start: 0.7440 (m-80) cc_final: 0.7226 (m-80) REVERT: H 87 ASN cc_start: 0.8786 (t0) cc_final: 0.8260 (t0) REVERT: H 96 GLU cc_start: 0.8555 (mp0) cc_final: 0.8199 (mp0) REVERT: H 116 GLU cc_start: 0.8281 (tp30) cc_final: 0.7797 (tp30) REVERT: Q 712 LYS cc_start: 0.8656 (pttp) cc_final: 0.8384 (tptt) REVERT: Q 838 MET cc_start: 0.5631 (ptt) cc_final: 0.5165 (ptp) REVERT: Q 944 LEU cc_start: 0.5625 (mp) cc_final: 0.5187 (mp) REVERT: Q 1005 MET cc_start: 0.7948 (mpp) cc_final: 0.7240 (ptp) REVERT: Q 1321 TYR cc_start: 0.8238 (m-80) cc_final: 0.7848 (m-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1541 time to fit residues: 39.3951 Evaluate side-chains 123 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** Q 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 769 ASN Q 874 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.064071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046585 restraints weight = 118528.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.047546 restraints weight = 71250.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.048190 restraints weight = 52414.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.048571 restraints weight = 43377.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.048826 restraints weight = 38802.944| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16325 Z= 0.235 Angle : 0.664 9.646 23318 Z= 0.378 Chirality : 0.040 0.158 2653 Planarity : 0.005 0.062 1944 Dihedral : 30.332 175.251 4491 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % 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 aren not related in a simple way. whole: -0.34 (0.24), residues: 1173 helix: 0.68 (0.19), residues: 744 sheet: -0.72 (0.67), residues: 60 loop : -1.97 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 93 TYR 0.020 0.002 TYR H 86 PHE 0.020 0.002 PHE E 67 TRP 0.026 0.002 TRP Q1361 HIS 0.008 0.002 HIS Q 768 Details of bonding type rmsd covalent geometry : bond 0.00513 (16325) covalent geometry : angle 0.66354 (23318) hydrogen bonds : bond 0.05667 ( 879) hydrogen bonds : angle 3.83213 ( 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 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.452 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: 0.8760 (pp20) cc_final: 0.8524 (pp20) REVERT: B 85 MET cc_start: 0.9025 (tpp) cc_final: 0.8344 (mmm) REVERT: B 89 TYR cc_start: 0.8577 (m-80) cc_final: 0.8204 (m-80) REVERT: D 96 GLU cc_start: 0.8727 (mp0) cc_final: 0.8478 (mp0) REVERT: D 108 GLU cc_start: 0.6794 (pp20) cc_final: 0.6367 (pp20) REVERT: E 81 ASP cc_start: 0.8469 (t70) cc_final: 0.8225 (t70) REVERT: E 105 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8035 (tm-30) REVERT: G 58 TYR cc_start: 0.9086 (t80) cc_final: 0.8741 (t80) REVERT: G 93 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8061 (tm-30) REVERT: H 49 LYS cc_start: 0.9612 (mmmm) cc_final: 0.9202 (mmmt) REVERT: H 71 ASP cc_start: 0.9282 (t0) cc_final: 0.9008 (t0) REVERT: H 74 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8407 (tm-30) REVERT: H 96 GLU cc_start: 0.8650 (mp0) cc_final: 0.8382 (mm-30) REVERT: H 116 GLU cc_start: 0.8476 (tp30) cc_final: 0.8141 (tp30) REVERT: H 123 LYS cc_start: 0.9380 (tttm) cc_final: 0.9111 (tttm) REVERT: Q 926 MET cc_start: 0.8142 (mmm) cc_final: 0.7618 (mmm) REVERT: Q 1005 MET cc_start: 0.8018 (mpp) cc_final: 0.7403 (mtp) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1482 time to fit residues: 31.5466 Evaluate side-chains 120 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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: 1.9990 chunk 17 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN F 28 GLN Q1323 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.065929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048314 restraints weight = 117067.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.049377 restraints weight = 70930.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050063 restraints weight = 51590.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050451 restraints weight = 42546.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.050722 restraints weight = 38035.745| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4242 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= 0.147 Angle : 0.587 7.108 23318 Z= 0.336 Chirality : 0.037 0.177 2653 Planarity : 0.004 0.056 1944 Dihedral : 30.009 175.648 4491 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % 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 aren not related in a simple way. whole: 0.00 (0.24), residues: 1173 helix: 0.99 (0.19), residues: 739 sheet: -0.64 (0.68), residues: 65 loop : -1.89 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 93 TYR 0.027 0.001 TYR H 86 PHE 0.021 0.001 PHE Q 813 TRP 0.022 0.002 TRP Q 787 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd covalent geometry : bond 0.00316 (16325) covalent geometry : angle 0.58746 (23318) hydrogen bonds : bond 0.03837 ( 879) hydrogen bonds : angle 3.48596 ( 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 167 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8357 (p0) cc_final: 0.8055 (p0) REVERT: B 64 GLU cc_start: 0.8812 (pp20) cc_final: 0.8575 (pp20) REVERT: B 85 MET cc_start: 0.8995 (tpp) cc_final: 0.8214 (mmm) REVERT: B 89 TYR cc_start: 0.8568 (m-80) cc_final: 0.8062 (m-80) REVERT: D 79 GLU cc_start: 0.8236 (tp30) cc_final: 0.8033 (tp30) REVERT: D 96 GLU cc_start: 0.8761 (mp0) cc_final: 0.8414 (mp0) REVERT: E 76 GLN cc_start: 0.9116 (pm20) cc_final: 0.8809 (pm20) REVERT: E 81 ASP cc_start: 0.8435 (t70) cc_final: 0.8159 (t70) REVERT: E 105 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8081 (tm-30) REVERT: G 58 TYR cc_start: 0.9028 (t80) cc_final: 0.8527 (t80) REVERT: G 95 ASN cc_start: 0.9273 (m-40) cc_final: 0.9000 (m-40) REVERT: H 45 TYR cc_start: 0.8547 (t80) cc_final: 0.7989 (t80) REVERT: H 49 LYS cc_start: 0.9581 (mmmm) cc_final: 0.9270 (mmmm) REVERT: H 74 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8307 (tm-30) REVERT: H 96 GLU cc_start: 0.8532 (mp0) cc_final: 0.8229 (mm-30) REVERT: H 111 LYS cc_start: 0.9292 (ptmm) cc_final: 0.9061 (pttm) REVERT: H 116 GLU cc_start: 0.8363 (tp30) cc_final: 0.7982 (tp30) REVERT: Q 928 LEU cc_start: 0.8632 (pt) cc_final: 0.8167 (mm) REVERT: Q 1005 MET cc_start: 0.8065 (mpp) cc_final: 0.7520 (mtp) REVERT: Q 1352 GLU cc_start: 0.9033 (pm20) cc_final: 0.8816 (mp0) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1416 time to fit residues: 32.7936 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 : 0.448 ------------------------------------------------------------------------------- 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: 1.9990 chunk 13 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 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 = 0.3667 r_free = 0.3667 target = 0.065458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047937 restraints weight = 116669.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.048947 restraints weight = 70786.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.049620 restraints weight = 51655.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.050020 restraints weight = 42547.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.050282 restraints weight = 37831.718| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16325 Z= 0.158 Angle : 0.597 6.377 23318 Z= 0.342 Chirality : 0.037 0.164 2653 Planarity : 0.004 0.054 1944 Dihedral : 29.927 175.244 4491 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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 aren not related in a simple way. whole: 0.08 (0.24), residues: 1173 helix: 1.03 (0.19), residues: 736 sheet: -0.65 (0.70), residues: 60 loop : -1.75 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 37 TYR 0.020 0.001 TYR H 86 PHE 0.018 0.001 PHE Q 813 TRP 0.015 0.001 TRP Q 800 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd covalent geometry : bond 0.00345 (16325) covalent geometry : angle 0.59696 (23318) hydrogen bonds : bond 0.04089 ( 879) hydrogen bonds : angle 3.48983 ( 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 165 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9110 (mppt) cc_final: 0.8905 (mmtm) REVERT: B 64 GLU cc_start: 0.8849 (pp20) cc_final: 0.8576 (pp20) REVERT: B 85 MET cc_start: 0.9001 (tpp) cc_final: 0.8132 (mmm) REVERT: B 89 TYR cc_start: 0.8683 (m-80) cc_final: 0.8177 (m-80) REVERT: D 79 GLU cc_start: 0.8296 (tp30) cc_final: 0.8080 (tp30) REVERT: E 76 GLN cc_start: 0.9180 (pm20) cc_final: 0.8854 (pm20) REVERT: E 81 ASP cc_start: 0.8496 (t70) cc_final: 0.8209 (t70) REVERT: E 105 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8129 (tm-30) REVERT: F 101 PHE cc_start: 0.9076 (m-80) cc_final: 0.8781 (m-80) REVERT: G 58 TYR cc_start: 0.9044 (t80) cc_final: 0.8688 (t80) REVERT: G 93 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7988 (tm-30) REVERT: G 95 ASN cc_start: 0.9307 (m-40) cc_final: 0.8861 (m-40) REVERT: H 45 TYR cc_start: 0.8539 (t80) cc_final: 0.7993 (t80) REVERT: H 49 LYS cc_start: 0.9577 (mmmm) cc_final: 0.9273 (mmmm) REVERT: H 71 ASP cc_start: 0.9269 (t0) cc_final: 0.8981 (t0) REVERT: H 74 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8378 (tm-30) REVERT: H 75 ARG cc_start: 0.8962 (ttm170) cc_final: 0.8048 (ttm170) REVERT: H 96 GLU cc_start: 0.8560 (mp0) cc_final: 0.8273 (mm-30) REVERT: H 111 LYS cc_start: 0.9302 (ptmm) cc_final: 0.9053 (pttm) REVERT: Q 926 MET cc_start: 0.7792 (mmm) cc_final: 0.6727 (mpp) REVERT: Q 928 LEU cc_start: 0.8639 (pt) cc_final: 0.8032 (mm) REVERT: Q 1005 MET cc_start: 0.8093 (mpp) cc_final: 0.7524 (mtp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1422 time to fit residues: 32.9396 Evaluate side-chains 131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: 0.7980 chunk 142 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.067396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.050781 restraints weight = 134085.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.051872 restraints weight = 80974.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.052603 restraints weight = 58824.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.053061 restraints weight = 48398.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.053226 restraints weight = 43068.168| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16325 Z= 0.146 Angle : 0.583 7.380 23318 Z= 0.332 Chirality : 0.037 0.161 2653 Planarity : 0.004 0.062 1944 Dihedral : 29.841 175.270 4491 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 aren not related in a simple way. whole: 0.18 (0.25), residues: 1173 helix: 1.11 (0.20), residues: 734 sheet: -0.60 (0.70), residues: 60 loop : -1.70 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 37 TYR 0.013 0.001 TYR H 86 PHE 0.018 0.001 PHE Q 813 TRP 0.016 0.001 TRP Q 800 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd covalent geometry : bond 0.00317 (16325) covalent geometry : angle 0.58275 (23318) hydrogen bonds : bond 0.03739 ( 879) hydrogen bonds : angle 3.41085 ( 2266) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLU cc_start: 0.8845 (pp20) cc_final: 0.8563 (pp20) REVERT: B 85 MET cc_start: 0.8944 (tpp) cc_final: 0.8156 (mmm) REVERT: B 89 TYR cc_start: 0.8689 (m-80) cc_final: 0.8155 (m-80) REVERT: D 79 GLU cc_start: 0.8259 (tp30) cc_final: 0.8041 (tp30) REVERT: E 76 GLN cc_start: 0.9223 (pm20) cc_final: 0.8922 (pm20) REVERT: E 81 ASP cc_start: 0.8354 (t70) cc_final: 0.8075 (t70) REVERT: E 105 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8076 (tm-30) REVERT: F 101 PHE cc_start: 0.9056 (m-80) cc_final: 0.8730 (m-80) REVERT: G 58 TYR cc_start: 0.8994 (t80) cc_final: 0.8623 (t80) REVERT: G 95 ASN cc_start: 0.9317 (m-40) cc_final: 0.8931 (m-40) REVERT: H 45 TYR cc_start: 0.8465 (t80) cc_final: 0.7922 (t80) REVERT: H 49 LYS cc_start: 0.9549 (mmmm) cc_final: 0.9247 (mmmm) REVERT: H 71 ASP cc_start: 0.9222 (t0) cc_final: 0.8884 (t0) REVERT: H 74 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8303 (tm-30) REVERT: H 75 ARG cc_start: 0.8870 (ttm170) cc_final: 0.7963 (ttm170) REVERT: H 82 LYS cc_start: 0.9260 (ptpp) cc_final: 0.8838 (ptpp) REVERT: H 96 GLU cc_start: 0.8494 (mp0) cc_final: 0.8277 (mm-30) REVERT: H 111 LYS cc_start: 0.9255 (ptmm) cc_final: 0.8978 (pttm) REVERT: Q 838 MET cc_start: 0.6397 (ptt) cc_final: 0.6172 (ptt) REVERT: Q 926 MET cc_start: 0.7951 (mmm) cc_final: 0.6871 (mpp) REVERT: Q 928 LEU cc_start: 0.8793 (pt) cc_final: 0.8181 (mm) REVERT: Q 1005 MET cc_start: 0.8061 (mpp) cc_final: 0.7561 (mtp) REVERT: Q 1321 TYR cc_start: 0.8603 (m-80) cc_final: 0.8253 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1477 time to fit residues: 34.2255 Evaluate side-chains 135 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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: 0.5980 chunk 16 optimal weight: 0.4980 chunk 103 optimal weight: 8.9990 chunk 117 optimal weight: 0.4980 chunk 101 optimal weight: 0.0870 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 69 optimal weight: 0.0870 chunk 67 optimal weight: 1.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 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 = 0.3718 r_free = 0.3718 target = 0.068351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.051787 restraints weight = 134251.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.052855 restraints weight = 81617.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.053605 restraints weight = 59115.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.054069 restraints weight = 48468.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.054285 restraints weight = 43012.597| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16325 Z= 0.137 Angle : 0.592 7.165 23318 Z= 0.335 Chirality : 0.037 0.173 2653 Planarity : 0.004 0.053 1944 Dihedral : 29.691 175.661 4491 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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 aren not related in a simple way. whole: 0.16 (0.25), residues: 1173 helix: 1.09 (0.19), residues: 742 sheet: -0.62 (0.71), residues: 65 loop : -1.79 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 72 TYR 0.012 0.001 TYR G 51 PHE 0.025 0.001 PHE E 78 TRP 0.018 0.001 TRP Q 800 HIS 0.004 0.001 HIS Q 814 Details of bonding type rmsd covalent geometry : bond 0.00290 (16325) covalent geometry : angle 0.59183 (23318) hydrogen bonds : bond 0.03480 ( 879) hydrogen bonds : angle 3.42874 ( 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 166 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9047 (mppt) cc_final: 0.8828 (mmtm) REVERT: B 85 MET cc_start: 0.8842 (tpp) cc_final: 0.8058 (mmm) REVERT: B 89 TYR cc_start: 0.8663 (m-80) cc_final: 0.8140 (m-80) REVERT: C 72 ARG cc_start: 0.9090 (ttm110) cc_final: 0.8417 (mtm110) REVERT: E 81 ASP cc_start: 0.8341 (t70) cc_final: 0.8015 (t70) REVERT: E 105 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8140 (tm-30) REVERT: F 68 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.8394 (ttm110) REVERT: F 101 PHE cc_start: 0.9047 (m-80) cc_final: 0.8758 (m-80) REVERT: G 58 TYR cc_start: 0.8983 (t80) cc_final: 0.8616 (t80) REVERT: G 95 ASN cc_start: 0.9337 (m-40) cc_final: 0.9026 (m-40) REVERT: H 45 TYR cc_start: 0.8390 (t80) cc_final: 0.7765 (t80) REVERT: H 49 LYS cc_start: 0.9552 (mmmm) cc_final: 0.9257 (mmmm) REVERT: H 74 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8216 (tm-30) REVERT: H 75 ARG cc_start: 0.8855 (ttm170) cc_final: 0.8206 (mtm180) REVERT: H 96 GLU cc_start: 0.8513 (mp0) cc_final: 0.7917 (mp0) REVERT: Q 926 MET cc_start: 0.7975 (mmm) cc_final: 0.6923 (mpp) REVERT: Q 928 LEU cc_start: 0.8704 (pt) cc_final: 0.8126 (mm) REVERT: Q 1005 MET cc_start: 0.8062 (mpp) cc_final: 0.7568 (mtp) REVERT: Q 1321 TYR cc_start: 0.8581 (m-80) cc_final: 0.8282 (m-80) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1488 time to fit residues: 34.2190 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 : 0.387 ------------------------------------------------------------------------------- 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: 5.9990 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.065122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048626 restraints weight = 135824.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.049569 restraints weight = 83377.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.050173 restraints weight = 61126.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.050642 restraints weight = 51126.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.050906 restraints weight = 45699.960| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16325 Z= 0.206 Angle : 0.651 10.556 23318 Z= 0.367 Chirality : 0.039 0.158 2653 Planarity : 0.004 0.053 1944 Dihedral : 29.994 174.179 4491 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.25), residues: 1173 helix: 0.93 (0.19), residues: 751 sheet: -0.75 (0.74), residues: 55 loop : -1.72 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 33 TYR 0.015 0.002 TYR F 89 PHE 0.017 0.002 PHE Q 813 TRP 0.012 0.002 TRP Q 800 HIS 0.007 0.002 HIS G 32 Details of bonding type rmsd covalent geometry : bond 0.00456 (16325) covalent geometry : angle 0.65051 (23318) hydrogen bonds : bond 0.05009 ( 879) hydrogen bonds : angle 3.73806 ( 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 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8470 (pttt) cc_final: 0.8183 (tptt) REVERT: A 64 LYS cc_start: 0.9208 (mppt) cc_final: 0.8999 (mmtm) REVERT: B 85 MET cc_start: 0.8797 (tpp) cc_final: 0.8014 (mmm) REVERT: B 89 TYR cc_start: 0.8702 (m-80) cc_final: 0.8215 (m-80) REVERT: C 72 ARG cc_start: 0.9012 (ttm110) cc_final: 0.8512 (mtm-85) REVERT: E 81 ASP cc_start: 0.8412 (t70) cc_final: 0.8107 (t70) REVERT: E 105 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8157 (tm-30) REVERT: F 101 PHE cc_start: 0.9030 (m-80) cc_final: 0.8728 (m-80) REVERT: G 105 GLN cc_start: 0.8194 (mp10) cc_final: 0.7815 (mp10) REVERT: H 45 TYR cc_start: 0.8444 (t80) cc_final: 0.8001 (t80) REVERT: H 49 LYS cc_start: 0.9575 (mmmm) cc_final: 0.9257 (mmmm) REVERT: H 71 ASP cc_start: 0.9163 (t70) cc_final: 0.8860 (t0) REVERT: H 74 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8260 (tm-30) REVERT: H 75 ARG cc_start: 0.8986 (ttm170) cc_final: 0.8516 (mtm180) REVERT: H 96 GLU cc_start: 0.8624 (mp0) cc_final: 0.8263 (mm-30) REVERT: H 123 LYS cc_start: 0.9344 (tttm) cc_final: 0.9038 (tttm) REVERT: Q 1005 MET cc_start: 0.8215 (mpp) cc_final: 0.7689 (mtp) REVERT: Q 1321 TYR cc_start: 0.8681 (m-80) cc_final: 0.8331 (m-80) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1446 time to fit residues: 29.3811 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 : 0.314 ------------------------------------------------------------------------------- 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: 0.9980 chunk 86 optimal weight: 10.0000 chunk 139 optimal weight: 0.3980 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 126 optimal weight: 0.0770 chunk 87 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 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 = 0.3684 r_free = 0.3684 target = 0.066753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.050266 restraints weight = 134305.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.051323 restraints weight = 81158.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.052045 restraints weight = 58852.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052493 restraints weight = 48378.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.052747 restraints weight = 43064.010| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16325 Z= 0.144 Angle : 0.601 7.750 23318 Z= 0.338 Chirality : 0.037 0.163 2653 Planarity : 0.004 0.053 1944 Dihedral : 29.748 174.989 4491 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 aren not related in a simple way. whole: 0.24 (0.25), residues: 1173 helix: 1.16 (0.19), residues: 745 sheet: -0.76 (0.69), residues: 60 loop : -1.76 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 96 TYR 0.012 0.001 TYR G 51 PHE 0.019 0.001 PHE Q 813 TRP 0.017 0.001 TRP Q 800 HIS 0.004 0.001 HIS Q 768 Details of bonding type rmsd covalent geometry : bond 0.00310 (16325) covalent geometry : angle 0.60057 (23318) hydrogen bonds : bond 0.03633 ( 879) hydrogen bonds : angle 3.50500 ( 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 145 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 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: A 42 LYS cc_start: 0.8438 (pttt) cc_final: 0.8123 (tptt) REVERT: A 64 LYS cc_start: 0.9106 (mppt) cc_final: 0.8856 (mmtm) REVERT: B 85 MET cc_start: 0.8784 (tpp) cc_final: 0.8095 (mmm) REVERT: B 89 TYR cc_start: 0.8747 (m-80) cc_final: 0.8233 (m-80) REVERT: C 72 ARG cc_start: 0.9111 (ttm110) cc_final: 0.8691 (mtm-85) REVERT: D 79 GLU cc_start: 0.8234 (tp30) cc_final: 0.8002 (tp30) REVERT: E 81 ASP cc_start: 0.8283 (t70) cc_final: 0.7886 (t70) REVERT: E 94 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7883 (tp30) REVERT: E 105 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8109 (tm-30) REVERT: F 89 TYR cc_start: 0.8030 (m-80) cc_final: 0.7793 (m-80) REVERT: F 101 PHE cc_start: 0.8970 (m-80) cc_final: 0.8750 (m-80) REVERT: G 58 TYR cc_start: 0.8938 (t80) cc_final: 0.8595 (t80) REVERT: G 95 ASN cc_start: 0.9381 (m-40) cc_final: 0.8994 (m-40) REVERT: G 105 GLN cc_start: 0.8218 (mp10) cc_final: 0.7742 (mp10) REVERT: H 45 TYR cc_start: 0.8386 (t80) cc_final: 0.7948 (t80) REVERT: H 49 LYS cc_start: 0.9547 (mmmm) cc_final: 0.9269 (mmmm) REVERT: H 71 ASP cc_start: 0.9106 (t70) cc_final: 0.8813 (t0) REVERT: H 74 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8234 (tm-30) REVERT: H 75 ARG cc_start: 0.8899 (ttm170) cc_final: 0.8445 (mtm180) REVERT: H 96 GLU cc_start: 0.8528 (mp0) cc_final: 0.8062 (mp0) REVERT: H 123 LYS cc_start: 0.9332 (tttm) cc_final: 0.9098 (tttm) REVERT: Q 926 MET cc_start: 0.7765 (mmm) cc_final: 0.6890 (mpp) REVERT: Q 928 LEU cc_start: 0.8906 (pt) cc_final: 0.8268 (mm) REVERT: Q 1005 MET cc_start: 0.8142 (mpp) cc_final: 0.7710 (mtp) REVERT: Q 1321 TYR cc_start: 0.8625 (m-80) cc_final: 0.8215 (m-80) REVERT: Q 1432 MET cc_start: 0.9143 (mpp) cc_final: 0.8842 (mpp) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1493 time to fit residues: 30.3923 Evaluate side-chains 121 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 69 optimal weight: 0.0870 chunk 103 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 33 optimal weight: 0.0670 overall best weight: 0.9098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.064540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.047170 restraints weight = 116887.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.048126 restraints weight = 70269.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.048774 restraints weight = 51323.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.049188 restraints weight = 42335.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.049438 restraints weight = 37693.359| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16325 Z= 0.154 Angle : 0.606 7.819 23318 Z= 0.341 Chirality : 0.037 0.162 2653 Planarity : 0.004 0.054 1944 Dihedral : 29.740 174.640 4491 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.10 % Allowed : 0.71 % Favored : 99.19 % 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 aren not related in a simple way. whole: 0.21 (0.25), residues: 1173 helix: 1.08 (0.19), residues: 757 sheet: -0.71 (0.74), residues: 55 loop : -1.71 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 96 TYR 0.012 0.001 TYR G 51 PHE 0.017 0.001 PHE Q 813 TRP 0.016 0.001 TRP Q 800 HIS 0.005 0.001 HIS Q 814 Details of bonding type rmsd covalent geometry : bond 0.00338 (16325) covalent geometry : angle 0.60573 (23318) hydrogen bonds : bond 0.03899 ( 879) hydrogen bonds : angle 3.50184 ( 2266) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3087.34 seconds wall clock time: 53 minutes 55.03 seconds (3235.03 seconds total)