Starting phenix.real_space_refine on Tue Jul 7 01:02:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mll_48375/07_2026/9mll_48375.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mll_48375/07_2026/9mll_48375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mll_48375/07_2026/9mll_48375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mll_48375/07_2026/9mll_48375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mll_48375/07_2026/9mll_48375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mll_48375/07_2026/9mll_48375.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 530 5.49 5 S 28 5.16 5 C 12580 2.51 5 N 4243 2.21 5 O 5258 1.98 5 H 18340 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40979 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1626 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1715 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1460 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1561 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "F" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1396 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1637 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1415 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "I" Number of atoms: 4326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 4326 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "J" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 4365 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "L" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1585 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "M" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1396 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "N" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1627 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "O" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1415 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "P" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "Q" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "R" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1691 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "S" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1450 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "X" Number of atoms: 4043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 4043 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Chain: "Y" Number of atoms: 4073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 4073 Classifications: {'DNA': 128} Link IDs: {'rna3p': 127} Time building chain proxies: 7.45, per 1000 atoms: 0.18 Number of scatterers: 40979 At special positions: 0 Unit cell: (136.74, 146.2, 116.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 28 16.00 P 530 15.00 O 5258 8.00 N 4243 7.00 C 12580 6.00 H 18340 1.00 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: 3.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2760 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 18 sheets defined 72.9% alpha, 2.6% beta 264 base pairs and 450 stacking pairs defined. Time for finding SS restraints: 8.81 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.557A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.894A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.529A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.047A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.633A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.377A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.645A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.725A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.722A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.539A pdb=" N GLN E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.685A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.695A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 78 removed outlier: 3.955A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.562A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.532A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 74 removed outlier: 3.592A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.648A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 removed outlier: 3.533A pdb=" N LYS G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.898A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.799A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 58 Processing helix chain 'L' and resid 64 through 80 removed outlier: 4.189A pdb=" N GLN L 77 " --> pdb=" O ARG L 73 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP L 78 " --> pdb=" O GLU L 74 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE L 79 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 115 removed outlier: 3.860A pdb=" N VAL L 90 " --> pdb=" O GLN L 86 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET L 91 " --> pdb=" O SER L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 132 Processing helix chain 'M' and resid 31 through 40 Processing helix chain 'M' and resid 50 through 77 removed outlier: 4.070A pdb=" N GLU M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 94 removed outlier: 3.724A pdb=" N VAL M 87 " --> pdb=" O THR M 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 23 Processing helix chain 'N' and resid 27 through 38 Processing helix chain 'N' and resid 46 through 74 removed outlier: 4.422A pdb=" N VAL N 50 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR N 51 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU N 66 " --> pdb=" O GLU N 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.537A pdb=" N LEU N 84 " --> pdb=" O ILE N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 98 Processing helix chain 'N' and resid 113 through 117 removed outlier: 3.503A pdb=" N LEU N 117 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 50 removed outlier: 3.593A pdb=" N GLN O 48 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL O 49 " --> pdb=" O VAL O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 85 removed outlier: 3.716A pdb=" N ASN O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 103 Processing helix chain 'O' and resid 104 through 123 Processing helix chain 'P' and resid 45 through 58 removed outlier: 3.657A pdb=" N ARG P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS P 57 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER P 58 " --> pdb=" O ARG P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 80 removed outlier: 4.314A pdb=" N ASP P 78 " --> pdb=" O GLU P 74 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 115 removed outlier: 3.755A pdb=" N VAL P 90 " --> pdb=" O GLN P 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET P 91 " --> pdb=" O SER P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 133 removed outlier: 3.637A pdb=" N ILE P 125 " --> pdb=" O MET P 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.602A pdb=" N ILE Q 30 " --> pdb=" O ILE Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 42 Processing helix chain 'Q' and resid 50 through 77 removed outlier: 3.917A pdb=" N GLU Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 95 removed outlier: 3.538A pdb=" N VAL Q 87 " --> pdb=" O THR Q 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 23 Processing helix chain 'R' and resid 27 through 37 removed outlier: 3.568A pdb=" N VAL R 31 " --> pdb=" O PRO R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 74 removed outlier: 3.695A pdb=" N LEU R 66 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 89 removed outlier: 3.592A pdb=" N LEU R 84 " --> pdb=" O ILE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 98 removed outlier: 3.564A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 50 Processing helix chain 'S' and resid 56 through 85 removed outlier: 3.889A pdb=" N ASN S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 103 Processing helix chain 'S' and resid 104 through 124 removed outlier: 3.552A pdb=" N LYS S 109 " --> pdb=" O GLY S 105 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.680A pdb=" N ARG A 84 " --> 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 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.267A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.914A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.086A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.323A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (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 'L' and resid 84 through 85 removed outlier: 6.655A pdb=" N ARG L 84 " --> pdb=" O VAL M 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AB3, first strand: chain 'N' and resid 43 through 44 removed outlier: 7.260A pdb=" N ARG N 43 " --> pdb=" O ILE O 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'N' and resid 78 through 79 Processing sheet with id=AB5, first strand: chain 'N' and resid 102 through 103 removed outlier: 6.969A pdb=" N THR N 102 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'P' and resid 84 through 85 removed outlier: 7.050A pdb=" N ARG P 84 " --> pdb=" O VAL Q 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'P' and resid 119 through 120 Processing sheet with id=AB8, first strand: chain 'R' and resid 43 through 44 removed outlier: 7.329A pdb=" N ARG R 43 " --> pdb=" O ILE S 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'R' and resid 78 through 79 759 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 680 hydrogen bonds 1360 hydrogen bond angles 0 basepair planarities 264 basepair parallelities 450 stacking parallelities Total time for adding SS restraints: 10.13 Time building geometry restraints manager: 5.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18332 1.03 - 1.23: 174 1.23 - 1.42: 10235 1.42 - 1.62: 13670 1.62 - 1.81: 48 Bond restraints: 42459 Sorted by residual: bond pdb=" C3' DT I 43 " pdb=" C2' DT I 43 " ideal model delta sigma weight residual 1.516 1.565 -0.049 8.00e-03 1.56e+04 3.82e+01 bond pdb=" C3' DT X 43 " pdb=" C2' DT X 43 " ideal model delta sigma weight residual 1.516 1.563 -0.047 8.00e-03 1.56e+04 3.53e+01 bond pdb=" C5' DT J -16 " pdb=" C4' DT J -16 " ideal model delta sigma weight residual 1.512 1.547 -0.035 7.00e-03 2.04e+04 2.49e+01 bond pdb=" C3' DG Y -44 " pdb=" C2' DG Y -44 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.28e+01 bond pdb=" C3' DC Y 53 " pdb=" C2' DC Y 53 " ideal model delta sigma weight residual 1.516 1.554 -0.038 8.00e-03 1.56e+04 2.21e+01 ... (remaining 42454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 68636 1.46 - 2.92: 7417 2.92 - 4.38: 647 4.38 - 5.84: 234 5.84 - 7.30: 25 Bond angle restraints: 76959 Sorted by residual: angle pdb=" O4' DG Y 27 " pdb=" C1' DG Y 27 " pdb=" N9 DG Y 27 " ideal model delta sigma weight residual 108.00 114.73 -6.73 7.00e-01 2.04e+00 9.24e+01 angle pdb=" O5' DT J -16 " pdb=" C5' DT J -16 " pdb=" C4' DT J -16 " ideal model delta sigma weight residual 109.40 116.37 -6.97 8.00e-01 1.56e+00 7.59e+01 angle pdb=" O4' DG J 27 " pdb=" C1' DG J 27 " pdb=" N9 DG J 27 " ideal model delta sigma weight residual 108.00 113.86 -5.86 7.00e-01 2.04e+00 7.02e+01 angle pdb=" O5' DT Y -16 " pdb=" C5' DT Y -16 " pdb=" C4' DT Y -16 " ideal model delta sigma weight residual 109.40 115.71 -6.31 8.00e-01 1.56e+00 6.23e+01 angle pdb=" O4' DA I -54 " pdb=" C1' DA I -54 " pdb=" N9 DA I -54 " ideal model delta sigma weight residual 108.00 102.70 5.30 7.00e-01 2.04e+00 5.73e+01 ... (remaining 76954 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12705 17.99 - 35.99: 2178 35.99 - 53.98: 1853 53.98 - 71.98: 877 71.98 - 89.97: 52 Dihedral angle restraints: 17665 sinusoidal: 12851 harmonic: 4814 Sorted by residual: dihedral pdb=" CA PRO R 110 " pdb=" C PRO R 110 " pdb=" N ASN R 111 " pdb=" CA ASN R 111 " ideal model delta harmonic sigma weight residual -180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA PRO G 110 " pdb=" C PRO G 110 " pdb=" N ASN G 111 " pdb=" CA ASN G 111 " ideal model delta harmonic sigma weight residual -180.00 -153.49 -26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER O 88 " pdb=" C SER O 88 " pdb=" N THR O 89 " pdb=" CA THR O 89 " ideal model delta harmonic sigma weight residual -180.00 -155.20 -24.80 0 5.00e+00 4.00e-02 2.46e+01 ... (remaining 17662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2793 0.061 - 0.121: 774 0.121 - 0.182: 314 0.182 - 0.242: 68 0.242 - 0.303: 15 Chirality restraints: 3964 Sorted by residual: chirality pdb=" C3' DC X -20 " pdb=" C4' DC X -20 " pdb=" O3' DC X -20 " pdb=" C2' DC X -20 " both_signs ideal model delta sigma weight residual False -2.73 -2.43 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' DC X -10 " pdb=" C4' DC X -10 " pdb=" O3' DC X -10 " pdb=" C2' DC X -10 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C3' DG X -7 " pdb=" C4' DG X -7 " pdb=" O3' DG X -7 " pdb=" C2' DG X -7 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 3961 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 7 " 0.060 2.00e-02 2.50e+03 3.21e-02 2.84e+01 pdb=" N1 DC I 7 " -0.081 2.00e-02 2.50e+03 pdb=" C2 DC I 7 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DC I 7 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC I 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 7 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC I 7 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DC I 7 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 7 " -0.008 2.00e-02 2.50e+03 pdb=" H5 DC I 7 " 0.005 2.00e-02 2.50e+03 pdb=" H6 DC I 7 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC X -21 " 0.059 2.00e-02 2.50e+03 3.21e-02 2.84e+01 pdb=" N1 DC X -21 " -0.081 2.00e-02 2.50e+03 pdb=" C2 DC X -21 " 0.021 2.00e-02 2.50e+03 pdb=" O2 DC X -21 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC X -21 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC X -21 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC X -21 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DC X -21 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC X -21 " -0.018 2.00e-02 2.50e+03 pdb=" H5 DC X -21 " 0.010 2.00e-02 2.50e+03 pdb=" H6 DC X -21 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -12 " 0.042 2.00e-02 2.50e+03 3.14e-02 2.71e+01 pdb=" N1 DC I -12 " -0.085 2.00e-02 2.50e+03 pdb=" C2 DC I -12 " 0.039 2.00e-02 2.50e+03 pdb=" O2 DC I -12 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DC I -12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I -12 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I -12 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC I -12 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC I -12 " -0.000 2.00e-02 2.50e+03 pdb=" H5 DC I -12 " 0.007 2.00e-02 2.50e+03 pdb=" H6 DC I -12 " 0.003 2.00e-02 2.50e+03 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1101 2.15 - 2.76: 64363 2.76 - 3.37: 105568 3.37 - 3.99: 142232 3.99 - 4.60: 220119 Nonbonded interactions: 533383 Sorted by model distance: nonbonded pdb=" OE1 GLU L 51 " pdb=" HE ARG M 40 " model vdw 1.534 2.450 nonbonded pdb=" O ILE A 63 " pdb="HE22 GLN A 94 " model vdw 1.541 2.450 nonbonded pdb=" OD2 ASP E 107 " pdb="HH11 ARG E 132 " model vdw 1.557 2.450 nonbonded pdb=" H GLY B 49 " pdb=" OP1 DC J 7 " model vdw 1.592 2.450 nonbonded pdb=" OD2 ASP L 107 " pdb="HH11 ARG L 132 " model vdw 1.593 2.450 ... (remaining 533378 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' and resid 42 through 134) selection = chain 'E' selection = (chain 'L' and resid 42 through 134) selection = (chain 'P' and resid 42 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 103) selection = (chain 'M' and resid 25 through 103) selection = chain 'Q' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = (chain 'G' and resid 16 through 118) selection = chain 'N' selection = (chain 'R' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 35 through 123) selection = chain 'H' selection = chain 'O' selection = (chain 'S' and resid 35 through 123) } ncs_group { reference = (chain 'I' and resid -67 through 58) selection = (chain 'X' and resid -67 through 58) } ncs_group { reference = (chain 'J' and resid -58 through 67) selection = (chain 'Y' and resid -58 through 67) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 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: 0.220 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 48.540 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5079 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 : 0.007 0.056 24119 Z= 0.619 Angle : 1.042 7.301 34840 Z= 0.858 Chirality : 0.069 0.303 3964 Planarity : 0.012 0.131 2575 Dihedral : 26.676 89.973 10350 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.85 % Favored : 98.08 % Rotamer: Outliers : 0.81 % Allowed : 9.43 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1456 helix: -0.09 (0.15), residues: 1009 sheet: None (None), residues: 0 loop : -0.38 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG H 93 TYR 0.034 0.004 TYR F 52 PHE 0.016 0.002 PHE L 105 HIS 0.009 0.003 HIS H 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.62 (24119) covalent geometry : angle 1.04222 / 0.86 (34840) hydrogen bonds : bond 0.10468 / 6.58 ( 1439) hydrogen bonds : angle 4.29727 / 3.15 ( 3613) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 628 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 30 ILE cc_start: 0.7701 (mm) cc_final: 0.7327 (mm) outliers start: 10 outliers final: 4 residues processed: 633 average time/residue: 0.4442 time to fit residues: 390.2316 Evaluate side-chains 418 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 414 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain M residue 80 LYS Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 79 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN B 65 ASN B 94 GLN D 50 HIS D 85 ASN D 96 GLN E 86 GLN H 110 HIS L 86 GLN M 94 GLN P 77 GLN P 86 GLN Q 26 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.094361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.072142 restraints weight = 298356.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.074521 restraints weight = 188825.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.076113 restraints weight = 137385.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.077274 restraints weight = 110718.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.078076 restraints weight = 94770.905| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 24119 Z= 0.214 Angle : 0.771 7.838 34840 Z= 0.486 Chirality : 0.048 0.182 3964 Planarity : 0.007 0.069 2575 Dihedral : 29.719 117.739 7440 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.01 % Allowed : 21.46 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.20), residues: 1456 helix: 1.03 (0.15), residues: 1039 sheet: None (None), residues: 0 loop : -0.37 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 80 TYR 0.018 0.002 TYR B 89 PHE 0.023 0.002 PHE S 71 HIS 0.014 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.21 (24119) covalent geometry : angle 0.77064 / 0.49 (34840) hydrogen bonds : bond 0.07180 / 4.72 ( 1439) hydrogen bonds : angle 3.96903 / 2.92 ( 3613) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 439 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8709 (mptt) REVERT: B 30 ILE cc_start: 0.8262 (mm) cc_final: 0.7776 (mm) REVERT: D 60 MET cc_start: 0.6572 (tpp) cc_final: 0.6363 (tpt) REVERT: F 63 LEU cc_start: 0.9739 (mt) cc_final: 0.9517 (mt) REVERT: G 111 ASN cc_start: 0.8635 (m-40) cc_final: 0.8423 (m-40) REVERT: L 105 PHE cc_start: 0.9475 (m-80) cc_final: 0.9174 (m-10) REVERT: R 58 TYR cc_start: 0.7826 (t80) cc_final: 0.7288 (t80) REVERT: R 65 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7254 (tm-30) REVERT: R 69 ASN cc_start: 0.7919 (m-40) cc_final: 0.7456 (m-40) outliers start: 37 outliers final: 23 residues processed: 452 average time/residue: 0.4168 time to fit residues: 267.5555 Evaluate side-chains 406 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 383 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 1 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 179 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 181 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 130 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.078191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.062377 restraints weight = 312493.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.064497 restraints weight = 163971.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.065894 restraints weight = 106347.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.066789 restraints weight = 79233.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.067420 restraints weight = 65202.983| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24119 Z= 0.192 Angle : 0.681 7.080 34840 Z= 0.449 Chirality : 0.043 0.206 3964 Planarity : 0.006 0.085 2575 Dihedral : 30.056 117.529 7431 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.17 % Allowed : 21.14 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.20), residues: 1456 helix: 1.28 (0.15), residues: 1037 sheet: None (None), residues: 0 loop : -0.40 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 18 TYR 0.015 0.002 TYR Q 73 PHE 0.013 0.002 PHE O 66 HIS 0.006 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.19 (24119) covalent geometry : angle 0.68068 / 0.45 (34840) hydrogen bonds : bond 0.06727 / 4.40 ( 1439) hydrogen bonds : angle 3.81378 / 2.81 ( 3613) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 402 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8164 (mm-30) REVERT: F 61 VAL cc_start: 0.9666 (m) cc_final: 0.9399 (p) REVERT: F 64 GLU cc_start: 0.9532 (mt-10) cc_final: 0.9327 (mt-10) REVERT: G 62 GLU cc_start: 0.9474 (tp30) cc_final: 0.9159 (tp30) REVERT: G 69 ASN cc_start: 0.8159 (t0) cc_final: 0.7829 (t0) REVERT: G 111 ASN cc_start: 0.8727 (m-40) cc_final: 0.8475 (m110) REVERT: N 18 ARG cc_start: 0.8500 (mtm180) cc_final: 0.8168 (mtp-110) REVERT: N 43 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7666 (mtm180) REVERT: N 111 ASN cc_start: 0.8430 (t0) cc_final: 0.7648 (m110) REVERT: P 79 PHE cc_start: 0.6942 (m-80) cc_final: 0.6722 (m-10) REVERT: R 65 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7276 (tm-30) REVERT: R 69 ASN cc_start: 0.7680 (m-40) cc_final: 0.6977 (m110) outliers start: 39 outliers final: 31 residues processed: 422 average time/residue: 0.4006 time to fit residues: 241.7304 Evaluate side-chains 404 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 373 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 89 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 81 optimal weight: 30.0000 chunk 18 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 175 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 40.0000 chunk 169 optimal weight: 30.0000 chunk 166 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 136 optimal weight: 10.0000 overall best weight: 6.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 48 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 = 0.4131 r_free = 0.4131 target = 0.073467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.058375 restraints weight = 362873.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.060190 restraints weight = 198189.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.061370 restraints weight = 134068.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.062114 restraints weight = 103592.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.062649 restraints weight = 88102.565| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 24119 Z= 0.263 Angle : 0.732 7.412 34840 Z= 0.462 Chirality : 0.043 0.169 3964 Planarity : 0.006 0.055 2575 Dihedral : 30.421 119.863 7431 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.15 % Allowed : 21.06 % Favored : 74.80 % 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 are not related in a simple way. whole: 0.38 (0.20), residues: 1456 helix: 0.72 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -0.75 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG L 132 TYR 0.021 0.002 TYR F 99 PHE 0.018 0.002 PHE S 71 HIS 0.012 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.26 (24119) covalent geometry : angle 0.73165 / 0.46 (34840) hydrogen bonds : bond 0.09136 / 6.03 ( 1439) hydrogen bonds : angle 4.17995 / 3.07 ( 3613) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 372 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8183 (mmm) cc_final: 0.7933 (mmp) REVERT: C 62 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7995 (mm-30) REVERT: D 66 PHE cc_start: 0.7049 (t80) cc_final: 0.6789 (t80) REVERT: E 77 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8411 (tp-100) REVERT: F 61 VAL cc_start: 0.9680 (m) cc_final: 0.9354 (p) REVERT: G 37 LYS cc_start: 0.9316 (mmtm) cc_final: 0.9092 (mmmt) REVERT: L 52 ILE cc_start: 0.8967 (tp) cc_final: 0.8541 (tp) REVERT: L 56 GLN cc_start: 0.9030 (mt0) cc_final: 0.8671 (mt0) REVERT: M 85 MET cc_start: 0.8865 (mmm) cc_final: 0.8480 (mmt) REVERT: N 111 ASN cc_start: 0.8756 (t0) cc_final: 0.8293 (m110) REVERT: P 55 TYR cc_start: 0.8876 (m-80) cc_final: 0.8285 (m-80) REVERT: R 36 ARG cc_start: 0.8978 (ttm110) cc_final: 0.8409 (mmm160) REVERT: R 58 TYR cc_start: 0.7673 (t80) cc_final: 0.7249 (t80) REVERT: R 62 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8433 (mm-30) REVERT: R 65 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7627 (tm-30) outliers start: 51 outliers final: 45 residues processed: 399 average time/residue: 0.3748 time to fit residues: 217.0968 Evaluate side-chains 392 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 346 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 44 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.074647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.058578 restraints weight = 351448.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.060464 restraints weight = 190800.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.061658 restraints weight = 128680.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.062395 restraints weight = 100270.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.062886 restraints weight = 85923.165| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24119 Z= 0.171 Angle : 0.657 6.211 34840 Z= 0.425 Chirality : 0.042 0.197 3964 Planarity : 0.005 0.060 2575 Dihedral : 30.482 118.944 7431 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.41 % Allowed : 23.33 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.21), residues: 1456 helix: 1.31 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : -0.74 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 68 TYR 0.014 0.001 TYR Q 73 PHE 0.013 0.002 PHE S 71 HIS 0.004 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.17 (24119) covalent geometry : angle 0.65661 / 0.43 (34840) hydrogen bonds : bond 0.06486 / 4.25 ( 1439) hydrogen bonds : angle 3.75992 / 2.76 ( 3613) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 369 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 56 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8354 (mm-40) REVERT: B 85 MET cc_start: 0.8213 (mmm) cc_final: 0.7921 (mmp) REVERT: C 62 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8026 (mm-30) REVERT: D 60 MET cc_start: 0.7085 (tpp) cc_final: 0.6858 (tpp) REVERT: D 66 PHE cc_start: 0.6963 (t80) cc_final: 0.6740 (t80) REVERT: G 37 LYS cc_start: 0.9284 (mmtm) cc_final: 0.9064 (mmmt) REVERT: G 62 GLU cc_start: 0.9579 (tp30) cc_final: 0.9229 (tp30) REVERT: G 73 ASP cc_start: 0.8404 (t0) cc_final: 0.8107 (m-30) REVERT: H 96 GLN cc_start: 0.9562 (OUTLIER) cc_final: 0.8945 (tp-100) REVERT: M 68 ARG cc_start: 0.8926 (ptp-170) cc_final: 0.8622 (ptp-170) REVERT: M 85 MET cc_start: 0.8865 (mmm) cc_final: 0.8510 (mmt) REVERT: N 111 ASN cc_start: 0.8696 (t0) cc_final: 0.8136 (m110) REVERT: P 55 TYR cc_start: 0.8813 (m-80) cc_final: 0.8013 (m-80) REVERT: P 95 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8228 (tt0) REVERT: Q 37 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8032 (mmp80) REVERT: R 65 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7321 (tm-30) REVERT: R 69 ASN cc_start: 0.7698 (m-40) cc_final: 0.7012 (m110) outliers start: 42 outliers final: 37 residues processed: 389 average time/residue: 0.3791 time to fit residues: 213.4474 Evaluate side-chains 387 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 349 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 156 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 119 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 33 optimal weight: 0.0470 chunk 2 optimal weight: 9.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.074282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.058276 restraints weight = 352075.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.060148 restraints weight = 190617.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.061335 restraints weight = 128784.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.062091 restraints weight = 100376.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.062539 restraints weight = 85783.505| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 24119 Z= 0.172 Angle : 0.645 6.896 34840 Z= 0.416 Chirality : 0.041 0.282 3964 Planarity : 0.005 0.058 2575 Dihedral : 30.475 119.915 7431 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.50 % Allowed : 23.50 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.21), residues: 1456 helix: 1.60 (0.15), residues: 1051 sheet: None (None), residues: 0 loop : -0.78 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 68 TYR 0.014 0.001 TYR E 100 PHE 0.012 0.002 PHE S 71 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 (24119) covalent geometry : angle 0.64547 / 0.42 (34840) hydrogen bonds : bond 0.05901 / 3.89 ( 1439) hydrogen bonds : angle 3.62146 / 2.66 ( 3613) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 363 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8318 (mm-40) REVERT: A 121 MET cc_start: 0.6200 (mtt) cc_final: 0.5936 (mtt) REVERT: B 85 MET cc_start: 0.8229 (mmm) cc_final: 0.7953 (mmp) REVERT: C 62 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7953 (mm-30) REVERT: C 65 GLU cc_start: 0.7855 (tp30) cc_final: 0.7603 (tp30) REVERT: D 66 PHE cc_start: 0.6903 (t80) cc_final: 0.6682 (t80) REVERT: G 37 LYS cc_start: 0.9278 (mmtm) cc_final: 0.9069 (mmmt) REVERT: G 62 GLU cc_start: 0.9589 (tp30) cc_final: 0.9249 (tp30) REVERT: G 73 ASP cc_start: 0.8399 (t0) cc_final: 0.8133 (m-30) REVERT: M 85 MET cc_start: 0.8924 (mmm) cc_final: 0.8610 (mmt) REVERT: N 111 ASN cc_start: 0.8751 (t0) cc_final: 0.8168 (m110) REVERT: P 55 TYR cc_start: 0.8819 (m-80) cc_final: 0.8013 (m-80) REVERT: Q 37 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8006 (mmp80) REVERT: R 58 TYR cc_start: 0.7762 (t80) cc_final: 0.7279 (t80) REVERT: R 62 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8479 (mm-30) REVERT: R 65 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7359 (tm-30) REVERT: R 69 ASN cc_start: 0.7754 (m-40) cc_final: 0.7069 (m110) outliers start: 43 outliers final: 36 residues processed: 384 average time/residue: 0.3550 time to fit residues: 197.6815 Evaluate side-chains 373 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 337 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 116 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 179 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 chunk 129 optimal weight: 0.0060 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.073949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.058540 restraints weight = 358547.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.060397 restraints weight = 194045.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.061592 restraints weight = 130380.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.062324 restraints weight = 100972.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.062860 restraints weight = 86245.916| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24119 Z= 0.164 Angle : 0.640 7.522 34840 Z= 0.411 Chirality : 0.041 0.208 3964 Planarity : 0.005 0.064 2575 Dihedral : 30.505 120.842 7431 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.50 % Allowed : 24.31 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.21), residues: 1456 helix: 1.66 (0.15), residues: 1055 sheet: None (None), residues: 0 loop : -0.74 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 100 TYR 0.013 0.001 TYR H 41 PHE 0.012 0.002 PHE E 79 HIS 0.006 0.001 HIS S 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.16 (24119) covalent geometry : angle 0.64048 / 0.41 (34840) hydrogen bonds : bond 0.05647 / 3.73 ( 1439) hydrogen bonds : angle 3.56026 / 2.62 ( 3613) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 344 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8240 (mm-40) REVERT: B 85 MET cc_start: 0.8229 (mmm) cc_final: 0.7969 (mmp) REVERT: C 62 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 60 MET cc_start: 0.6968 (tpp) cc_final: 0.6697 (tpp) REVERT: G 37 LYS cc_start: 0.9292 (mmtm) cc_final: 0.9087 (mmmt) REVERT: G 62 GLU cc_start: 0.9593 (tp30) cc_final: 0.9247 (tp30) REVERT: G 73 ASP cc_start: 0.8381 (t0) cc_final: 0.8132 (m-30) REVERT: H 96 GLN cc_start: 0.9536 (tt0) cc_final: 0.8891 (tp-100) REVERT: L 56 GLN cc_start: 0.8958 (mt0) cc_final: 0.8466 (mt0) REVERT: M 85 MET cc_start: 0.8862 (mmm) cc_final: 0.8540 (mmt) REVERT: N 111 ASN cc_start: 0.8735 (t0) cc_final: 0.8176 (m110) REVERT: P 55 TYR cc_start: 0.8798 (m-80) cc_final: 0.7991 (m-80) REVERT: Q 37 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.7979 (mmp80) REVERT: R 58 TYR cc_start: 0.7724 (t80) cc_final: 0.7144 (t80) REVERT: R 62 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8482 (mm-30) REVERT: R 65 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7260 (tm-30) REVERT: R 69 ASN cc_start: 0.7783 (m-40) cc_final: 0.7065 (m110) outliers start: 43 outliers final: 41 residues processed: 364 average time/residue: 0.3436 time to fit residues: 184.1209 Evaluate side-chains 380 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 339 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 89 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 0.0070 chunk 47 optimal weight: 0.0270 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 overall best weight: 2.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.073175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.058176 restraints weight = 335788.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.060149 restraints weight = 174524.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.061435 restraints weight = 113174.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.062275 restraints weight = 84734.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.062870 restraints weight = 70228.489| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.6284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24119 Z= 0.161 Angle : 0.630 7.352 34840 Z= 0.404 Chirality : 0.040 0.182 3964 Planarity : 0.005 0.118 2575 Dihedral : 30.517 122.271 7431 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.25 % Allowed : 24.88 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.21), residues: 1456 helix: 1.84 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -0.70 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 93 TYR 0.016 0.001 TYR Q 89 PHE 0.011 0.001 PHE D 66 HIS 0.005 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.16 (24119) covalent geometry : angle 0.62996 / 0.40 (34840) hydrogen bonds : bond 0.05357 / 3.53 ( 1439) hydrogen bonds : angle 3.45726 / 2.55 ( 3613) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 352 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8268 (mmm) cc_final: 0.8039 (mmp) REVERT: C 62 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8028 (mm-30) REVERT: F 54 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8147 (mp0) REVERT: G 37 LYS cc_start: 0.9293 (mmtm) cc_final: 0.9090 (mmmt) REVERT: G 62 GLU cc_start: 0.9584 (tp30) cc_final: 0.9262 (tp30) REVERT: G 73 ASP cc_start: 0.8372 (t0) cc_final: 0.8118 (m-30) REVERT: H 96 GLN cc_start: 0.9571 (tt0) cc_final: 0.8963 (tp-100) REVERT: M 85 MET cc_start: 0.8899 (mmm) cc_final: 0.8574 (mmt) REVERT: N 111 ASN cc_start: 0.8781 (t0) cc_final: 0.8203 (m110) REVERT: P 55 TYR cc_start: 0.8795 (m-80) cc_final: 0.7997 (m-80) REVERT: Q 37 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.7926 (mmp80) REVERT: R 58 TYR cc_start: 0.7741 (t80) cc_final: 0.7166 (t80) REVERT: R 62 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8483 (mm-30) REVERT: R 65 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7301 (tm-30) REVERT: R 69 ASN cc_start: 0.7795 (m-40) cc_final: 0.7067 (m110) outliers start: 40 outliers final: 40 residues processed: 370 average time/residue: 0.3592 time to fit residues: 195.5576 Evaluate side-chains 377 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 186 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 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 = 0.4107 r_free = 0.4107 target = 0.071320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.055795 restraints weight = 369634.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.057550 restraints weight = 202894.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.058651 restraints weight = 138513.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.059337 restraints weight = 108874.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.059800 restraints weight = 93719.955| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24119 Z= 0.212 Angle : 0.669 9.753 34840 Z= 0.423 Chirality : 0.041 0.192 3964 Planarity : 0.005 0.089 2575 Dihedral : 30.585 122.950 7431 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.74 % Allowed : 24.80 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1456 helix: 1.42 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -0.93 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 100 TYR 0.030 0.002 TYR S 84 PHE 0.021 0.002 PHE E 79 HIS 0.006 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.21 (24119) covalent geometry : angle 0.66929 / 0.42 (34840) hydrogen bonds : bond 0.07247 / 4.80 ( 1439) hydrogen bonds : angle 3.79734 / 2.79 ( 3613) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8324 (mmm) cc_final: 0.8073 (mmp) REVERT: C 62 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8049 (mm-30) REVERT: D 60 MET cc_start: 0.7107 (tpp) cc_final: 0.6871 (tpp) REVERT: F 74 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8976 (p) REVERT: G 62 GLU cc_start: 0.9595 (tp30) cc_final: 0.9294 (tp30) REVERT: G 73 ASP cc_start: 0.8501 (t0) cc_final: 0.8172 (m-30) REVERT: H 96 GLN cc_start: 0.9595 (tt0) cc_final: 0.8958 (tp-100) REVERT: H 100 ARG cc_start: 0.9165 (ttm110) cc_final: 0.8841 (ttm110) REVERT: L 77 GLN cc_start: 0.9203 (pt0) cc_final: 0.8982 (pm20) REVERT: N 111 ASN cc_start: 0.8828 (t0) cc_final: 0.8220 (m110) REVERT: P 55 TYR cc_start: 0.8853 (m-80) cc_final: 0.8075 (m-80) REVERT: Q 37 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.7940 (mmp80) REVERT: R 58 TYR cc_start: 0.7765 (t80) cc_final: 0.7077 (t80) REVERT: R 62 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8423 (mm-30) REVERT: R 65 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7359 (tm-30) REVERT: R 69 ASN cc_start: 0.7846 (m-40) cc_final: 0.7184 (m110) outliers start: 46 outliers final: 41 residues processed: 346 average time/residue: 0.3744 time to fit residues: 190.3783 Evaluate side-chains 356 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 314 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 132 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 182 optimal weight: 30.0000 chunk 122 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.072694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.057547 restraints weight = 367563.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.059359 restraints weight = 197956.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.060522 restraints weight = 133708.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.061273 restraints weight = 103707.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.061740 restraints weight = 88359.723| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24119 Z= 0.155 Angle : 0.641 7.599 34840 Z= 0.407 Chirality : 0.040 0.187 3964 Planarity : 0.005 0.065 2575 Dihedral : 30.611 123.739 7431 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.76 % Allowed : 25.61 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.21), residues: 1456 helix: 1.82 (0.16), residues: 1055 sheet: None (None), residues: 0 loop : -0.81 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 100 TYR 0.024 0.001 TYR S 84 PHE 0.023 0.002 PHE H 66 HIS 0.005 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.15 (24119) covalent geometry : angle 0.64066 / 0.41 (34840) hydrogen bonds : bond 0.05205 / 3.42 ( 1439) hydrogen bonds : angle 3.44202 / 2.54 ( 3613) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2912 Ramachandran restraints generated. 1456 Oldfield, 0 Emsley, 1456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 332 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8240 (mmm) cc_final: 0.7993 (mmp) REVERT: C 62 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8061 (mm-30) REVERT: C 65 GLU cc_start: 0.7610 (tp30) cc_final: 0.7153 (tm-30) REVERT: G 62 GLU cc_start: 0.9589 (tp30) cc_final: 0.9273 (tp30) REVERT: G 73 ASP cc_start: 0.8474 (t0) cc_final: 0.8158 (m-30) REVERT: L 77 GLN cc_start: 0.9174 (pt0) cc_final: 0.8948 (pm20) REVERT: M 85 MET cc_start: 0.8884 (mmm) cc_final: 0.8654 (mmt) REVERT: N 111 ASN cc_start: 0.8841 (t0) cc_final: 0.8218 (m110) REVERT: P 80 LYS cc_start: 0.8516 (tptp) cc_final: 0.8017 (tptp) REVERT: Q 37 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.7685 (mmp80) REVERT: Q 101 PHE cc_start: 0.8321 (m-80) cc_final: 0.8023 (m-80) REVERT: R 58 TYR cc_start: 0.7737 (t80) cc_final: 0.7290 (t80) REVERT: R 62 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8547 (mm-30) REVERT: R 65 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7440 (tm-30) REVERT: R 69 ASN cc_start: 0.7872 (m-40) cc_final: 0.7179 (m110) outliers start: 34 outliers final: 33 residues processed: 348 average time/residue: 0.3599 time to fit residues: 183.4683 Evaluate side-chains 361 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 328 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 66 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 140 optimal weight: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 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 = 0.4088 r_free = 0.4088 target = 0.070401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.054983 restraints weight = 371328.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.056717 restraints weight = 204183.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.057813 restraints weight = 139696.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.058514 restraints weight = 110133.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.058970 restraints weight = 94480.282| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24119 Z= 0.204 Angle : 0.662 7.878 34840 Z= 0.419 Chirality : 0.041 0.191 3964 Planarity : 0.005 0.071 2575 Dihedral : 30.625 123.529 7431 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.85 % Allowed : 25.93 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1456 helix: 1.50 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -0.90 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 100 TYR 0.025 0.002 TYR S 84 PHE 0.022 0.002 PHE H 66 HIS 0.008 0.002 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.20 (24119) covalent geometry : angle 0.66206 / 0.42 (34840) hydrogen bonds : bond 0.07148 / 4.74 ( 1439) hydrogen bonds : angle 3.75251 / 2.76 ( 3613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7561.64 seconds wall clock time: 129 minutes 14.12 seconds (7754.12 seconds total)