Starting phenix.real_space_refine on Tue Sep 15 15:53:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mll_48375/09_2026/9mll_48375.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mll_48375/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mll_48375/09_2026/9mll_48375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mll_48375/09_2026/9mll_48375.map" model { file = "/net/cci-nas-00/data/ceres_data/9mll_48375/09_2026/9mll_48375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mll_48375/09_2026/9mll_48375.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-2.2.1-6174/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: 6.63, per 1000 atoms: 0.16 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: 3.66 Conformation dependent library (CDL) restraints added in 786.0 milliseconds 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: 6.86 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: 9.53 Time building geometry restraints manager: 5.07 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: 68525 1.46 - 2.92: 7509 2.92 - 4.38: 665 4.38 - 5.84: 235 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: 2.400 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: 0.230 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 41.890 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.310 ------------------------------------------------------------------------------- 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 : 1.051 7.301 34840 Z= 0.867 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 1.05062 / 0.87 (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 : 0.849 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.7701 (mm) cc_final: 0.7327 (mm) REVERT: S 89 THR cc_start: 0.5764 (t) cc_final: 0.5452 (p) outliers start: 10 outliers final: 4 residues processed: 633 average time/residue: 0.4436 time to fit residues: 392.6145 Evaluate side-chains 424 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 420 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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: 0.6980 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 GLN B 65 ASN B 94 GLN C 39 HIS 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.093642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.071784 restraints weight = 291688.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.074172 restraints weight = 183695.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.075771 restraints weight = 133323.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.076943 restraints weight = 106762.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.077738 restraints weight = 90413.753| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 24119 Z= 0.217 Angle : 0.765 7.618 34840 Z= 0.486 Chirality : 0.048 0.181 3964 Planarity : 0.007 0.065 2575 Dihedral : 29.671 114.278 7440 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.85 % Allowed : 21.30 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.20), residues: 1456 helix: 1.06 (0.15), residues: 1038 sheet: None (None), residues: 0 loop : -0.33 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 36 TYR 0.021 0.002 TYR B 89 PHE 0.022 0.002 PHE S 71 HIS 0.012 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.22 (24119) covalent geometry : angle 0.76523 / 0.49 (34840) hydrogen bonds : bond 0.07120 / 4.67 ( 1439) hydrogen bonds : angle 3.97410 / 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 477 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 442 time to evaluate : 0.879 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: A 80 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8718 (mptt) REVERT: B 30 ILE cc_start: 0.8268 (mm) cc_final: 0.7805 (mm) REVERT: C 58 TYR cc_start: 0.7234 (t80) cc_final: 0.6597 (t80) REVERT: C 62 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7681 (mm-30) REVERT: L 105 PHE cc_start: 0.9538 (m-80) cc_final: 0.9227 (m-10) REVERT: N 42 GLU cc_start: 0.6803 (pm20) cc_final: 0.6474 (pm20) REVERT: N 43 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7665 (mtm180) REVERT: R 58 TYR cc_start: 0.7885 (t80) cc_final: 0.7500 (t80) REVERT: R 65 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7300 (tm-30) REVERT: R 69 ASN cc_start: 0.7932 (m-40) cc_final: 0.7497 (m-40) outliers start: 35 outliers final: 21 residues processed: 454 average time/residue: 0.4238 time to fit residues: 272.2456 Evaluate side-chains 410 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 389 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 1 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 172 optimal weight: 30.0000 chunk 179 optimal weight: 30.0000 chunk 140 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 32 HIS ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.074294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.058673 restraints weight = 360115.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.060514 restraints weight = 195491.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.061691 restraints weight = 132909.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.062433 restraints weight = 102766.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.062957 restraints weight = 87503.951| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24119 Z= 0.299 Angle : 0.764 6.986 34840 Z= 0.492 Chirality : 0.046 0.330 3964 Planarity : 0.006 0.099 2575 Dihedral : 30.237 115.717 7431 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.31 % Allowed : 20.24 % Favored : 75.45 % 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: -0.04 (0.20), residues: 1456 helix: 0.33 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.65 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 80 TYR 0.020 0.002 TYR H 41 PHE 0.019 0.003 PHE B 62 HIS 0.007 0.002 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.30 (24119) covalent geometry : angle 0.76359 / 0.49 (34840) hydrogen bonds : bond 0.10104 / 6.63 ( 1439) hydrogen bonds : angle 4.45677 / 3.27 ( 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 440 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 387 time to evaluate : 0.808 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: A 56 GLN cc_start: 0.8959 (mt0) cc_final: 0.8729 (mt0) REVERT: C 62 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7779 (mm-30) REVERT: F 61 VAL cc_start: 0.9662 (m) cc_final: 0.9340 (p) REVERT: F 99 TYR cc_start: 0.6746 (OUTLIER) cc_final: 0.6516 (m-80) REVERT: G 37 LYS cc_start: 0.9336 (mmtm) cc_final: 0.9107 (mmmt) REVERT: G 69 ASN cc_start: 0.8212 (t0) cc_final: 0.7922 (t0) REVERT: H 96 GLN cc_start: 0.9507 (tt0) cc_final: 0.8936 (tp40) REVERT: H 100 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8889 (ttm110) REVERT: M 68 ARG cc_start: 0.9029 (ptp-170) cc_final: 0.8792 (ptp-170) REVERT: N 57 GLU cc_start: 0.9052 (tt0) cc_final: 0.8675 (tt0) REVERT: N 111 ASN cc_start: 0.8648 (t0) cc_final: 0.8221 (m110) REVERT: O 96 GLN cc_start: 0.9547 (tt0) cc_final: 0.9234 (tp40) REVERT: P 79 PHE cc_start: 0.7136 (m-80) cc_final: 0.6905 (m-10) REVERT: Q 37 ARG cc_start: 0.8592 (mtm-85) cc_final: 0.7969 (mmp80) REVERT: R 69 ASN cc_start: 0.7576 (m-40) cc_final: 0.6918 (m110) outliers start: 53 outliers final: 41 residues processed: 413 average time/residue: 0.3925 time to fit residues: 232.8230 Evaluate side-chains 392 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 350 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 26 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 83 HIS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 114 GLU 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 F residue 21 LYS Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain G residue 60 THR 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 72 VAL 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 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 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 91 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: 9.9990 chunk 32 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 77 optimal weight: 40.0000 chunk 169 optimal weight: 30.0000 chunk 166 optimal weight: 40.0000 chunk 85 optimal weight: 30.0000 chunk 13 optimal weight: 0.4980 chunk 136 optimal weight: 8.9990 overall best weight: 7.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS O 68 ASN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.071999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.056791 restraints weight = 367187.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.058611 restraints weight = 196875.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.059775 restraints weight = 131869.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.060542 restraints weight = 101878.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.061008 restraints weight = 86382.152| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 24119 Z= 0.257 Angle : 0.736 8.453 34840 Z= 0.467 Chirality : 0.044 0.193 3964 Planarity : 0.007 0.090 2575 Dihedral : 30.533 116.792 7431 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.15 % Allowed : 22.20 % Favored : 73.66 % 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: -0.10 (0.20), residues: 1456 helix: 0.39 (0.15), residues: 1049 sheet: None (None), residues: 0 loop : -1.03 (0.26), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 132 TYR 0.023 0.002 TYR M 89 PHE 0.019 0.002 PHE H 66 HIS 0.009 0.002 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.26 (24119) covalent geometry : angle 0.73599 / 0.47 (34840) hydrogen bonds : bond 0.08942 / 5.87 ( 1439) hydrogen bonds : angle 4.38119 / 3.21 ( 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 420 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 0.748 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: B 85 MET cc_start: 0.8226 (mmm) cc_final: 0.7970 (mmp) REVERT: C 58 TYR cc_start: 0.7341 (t80) cc_final: 0.6595 (t80) REVERT: C 62 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7874 (mm-30) REVERT: F 99 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: G 37 LYS cc_start: 0.9337 (mmtm) cc_final: 0.9121 (mmmt) REVERT: G 69 ASN cc_start: 0.8283 (t0) cc_final: 0.8064 (t0) REVERT: M 68 ARG cc_start: 0.9045 (ptp-170) cc_final: 0.8786 (ptp-170) REVERT: M 85 MET cc_start: 0.8838 (mmm) cc_final: 0.8453 (mmt) REVERT: N 42 GLU cc_start: 0.7205 (pm20) cc_final: 0.6925 (pp20) REVERT: N 57 GLU cc_start: 0.9103 (tt0) cc_final: 0.8531 (tt0) REVERT: N 111 ASN cc_start: 0.8880 (t0) cc_final: 0.8192 (m110) REVERT: O 60 MET cc_start: 0.7551 (tmm) cc_final: 0.7275 (tpt) REVERT: P 55 TYR cc_start: 0.8862 (m-80) cc_final: 0.8194 (m-80) REVERT: Q 37 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8220 (mmt180) REVERT: R 58 TYR cc_start: 0.7659 (t80) cc_final: 0.7131 (t80) REVERT: R 62 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8397 (mm-30) outliers start: 51 outliers final: 43 residues processed: 394 average time/residue: 0.3908 time to fit residues: 222.3266 Evaluate side-chains 384 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 340 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 83 HIS 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 56 GLN 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 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 35 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 50 VAL 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 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 77 THR Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain P residue 113 ILE Chi-restraints excluded: chain Q residue 67 ILE 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 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: 10.0000 chunk 145 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.072191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.056908 restraints weight = 366420.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.058721 restraints weight = 197084.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.059868 restraints weight = 132412.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.060585 restraints weight = 102861.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.061093 restraints weight = 87984.547| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24119 Z= 0.194 Angle : 0.681 6.603 34840 Z= 0.438 Chirality : 0.042 0.171 3964 Planarity : 0.005 0.063 2575 Dihedral : 30.582 115.453 7431 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.98 % Allowed : 23.25 % Favored : 72.76 % 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: 0.54 (0.20), residues: 1456 helix: 0.93 (0.15), residues: 1043 sheet: None (None), residues: 0 loop : -0.98 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 68 TYR 0.015 0.002 TYR H 41 PHE 0.013 0.002 PHE D 66 HIS 0.005 0.001 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.19 (24119) covalent geometry : angle 0.68139 / 0.44 (34840) hydrogen bonds : bond 0.07337 / 4.82 ( 1439) hydrogen bonds : angle 3.98752 / 2.91 ( 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 409 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 360 time to evaluate : 0.794 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: A 56 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8412 (mm-40) REVERT: B 85 MET cc_start: 0.8208 (mmm) cc_final: 0.7933 (mmp) REVERT: C 58 TYR cc_start: 0.7317 (t80) cc_final: 0.6698 (t80) REVERT: C 62 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7935 (mm-30) REVERT: F 74 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8920 (p) REVERT: G 37 LYS cc_start: 0.9333 (mmtm) cc_final: 0.9118 (mmmt) REVERT: G 62 GLU cc_start: 0.9522 (tp30) cc_final: 0.9117 (tp30) REVERT: G 69 ASN cc_start: 0.8314 (t0) cc_final: 0.8056 (t0) REVERT: G 73 ASP cc_start: 0.7552 (m-30) cc_final: 0.7335 (m-30) REVERT: H 37 SER cc_start: 0.6184 (OUTLIER) cc_final: 0.5798 (p) REVERT: L 121 MET cc_start: 0.5507 (mtt) cc_final: 0.5306 (mtt) REVERT: M 68 ARG cc_start: 0.9010 (ptp-170) cc_final: 0.8743 (ptp-170) REVERT: M 85 MET cc_start: 0.8764 (mmm) cc_final: 0.8399 (mmt) REVERT: N 42 GLU cc_start: 0.6801 (pm20) cc_final: 0.6554 (pp20) REVERT: N 57 GLU cc_start: 0.9085 (tt0) cc_final: 0.8513 (tt0) REVERT: O 60 MET cc_start: 0.7573 (tmm) cc_final: 0.7324 (tpt) REVERT: P 55 TYR cc_start: 0.8801 (m-80) cc_final: 0.8014 (m-80) REVERT: Q 37 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8014 (mmp80) REVERT: R 58 TYR cc_start: 0.7577 (t80) cc_final: 0.7191 (t80) REVERT: R 62 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8568 (mm-30) REVERT: R 65 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7121 (tm-30) outliers start: 49 outliers final: 42 residues processed: 386 average time/residue: 0.3885 time to fit residues: 219.2262 Evaluate side-chains 385 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 83 HIS 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 56 GLN Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 74 GLU 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 26 ASN Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 69 ASP 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 47 VAL 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 35 LEU 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 69 ASP Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 67 ILE 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 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 156 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 119 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 90 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.071103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.055587 restraints weight = 367132.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.057367 restraints weight = 196668.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.058504 restraints weight = 132549.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.059233 restraints weight = 103080.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.059666 restraints weight = 88142.183| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24119 Z= 0.197 Angle : 0.673 7.565 34840 Z= 0.430 Chirality : 0.042 0.163 3964 Planarity : 0.005 0.046 2575 Dihedral : 30.612 117.122 7431 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.90 % Allowed : 24.39 % Favored : 71.71 % 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: 0.71 (0.21), residues: 1456 helix: 1.09 (0.15), residues: 1041 sheet: None (None), residues: 0 loop : -1.02 (0.26), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 68 TYR 0.023 0.002 TYR E 100 PHE 0.013 0.002 PHE S 71 HIS 0.006 0.001 HIS F 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.20 (24119) covalent geometry : angle 0.67322 / 0.43 (34840) hydrogen bonds : bond 0.07119 / 4.67 ( 1439) hydrogen bonds : angle 3.93639 / 2.88 ( 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 394 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 346 time to evaluate : 0.915 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: 0.8284 (mmm) cc_final: 0.8052 (mmp) REVERT: C 58 TYR cc_start: 0.7440 (t80) cc_final: 0.6595 (t80) REVERT: C 62 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7765 (mm-30) REVERT: D 63 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6890 (mmm) REVERT: F 74 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8933 (p) REVERT: G 37 LYS cc_start: 0.9355 (mmtm) cc_final: 0.9150 (mmmt) REVERT: G 69 ASN cc_start: 0.8281 (t0) cc_final: 0.7998 (t0) REVERT: L 121 MET cc_start: 0.5351 (mtt) cc_final: 0.5125 (mtt) REVERT: M 68 ARG cc_start: 0.9021 (ptp-170) cc_final: 0.8758 (ptp-170) REVERT: M 85 MET cc_start: 0.8804 (mmm) cc_final: 0.8520 (mmt) REVERT: O 60 MET cc_start: 0.7490 (tmm) cc_final: 0.7275 (tpt) REVERT: P 55 TYR cc_start: 0.8818 (m-80) cc_final: 0.8019 (m-80) REVERT: Q 37 ARG cc_start: 0.8603 (mtm-85) cc_final: 0.7963 (mmp80) REVERT: R 58 TYR cc_start: 0.7691 (t80) cc_final: 0.7246 (t80) REVERT: R 62 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8554 (mm-30) outliers start: 48 outliers final: 40 residues processed: 371 average time/residue: 0.3840 time to fit residues: 206.8299 Evaluate side-chains 371 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 329 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 63 MET Chi-restraints excluded: chain D residue 83 HIS 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 D residue 123 THR Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 119 THR 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 74 THR 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 96 GLN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE 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 69 ASP Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 107 LEU Chi-restraints excluded: chain P residue 75 ILE 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 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 116 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 110 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 179 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.071980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.056364 restraints weight = 365512.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.058190 restraints weight = 194808.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.059343 restraints weight = 130974.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.060057 restraints weight = 101995.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.060547 restraints weight = 87401.471| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24119 Z= 0.159 Angle : 0.645 7.417 34840 Z= 0.415 Chirality : 0.041 0.172 3964 Planarity : 0.005 0.077 2575 Dihedral : 30.606 117.572 7431 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.01 % Allowed : 25.93 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1456 helix: 1.49 (0.15), residues: 1045 sheet: None (None), residues: 0 loop : -0.89 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 68 TYR 0.014 0.001 TYR H 41 PHE 0.014 0.002 PHE D 66 HIS 0.004 0.001 HIS O 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.16 (24119) covalent geometry : angle 0.64549 / 0.42 (34840) hydrogen bonds : bond 0.05885 / 3.85 ( 1439) hydrogen bonds : angle 3.64643 / 2.67 ( 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 388 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 351 time to evaluate : 0.812 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: 0.8255 (mmm) cc_final: 0.7999 (mmp) REVERT: C 58 TYR cc_start: 0.7414 (t80) cc_final: 0.6694 (t80) REVERT: C 62 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7899 (mm-30) REVERT: F 74 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8930 (p) REVERT: G 37 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9129 (mmmt) REVERT: G 62 GLU cc_start: 0.9587 (tp30) cc_final: 0.9288 (tp30) REVERT: M 85 MET cc_start: 0.8817 (mmm) cc_final: 0.8485 (mmt) REVERT: Q 37 ARG cc_start: 0.8576 (mtm-85) cc_final: 0.7769 (mmp80) REVERT: R 58 TYR cc_start: 0.7680 (t80) cc_final: 0.7223 (t80) REVERT: R 62 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8568 (mm-30) REVERT: S 60 MET cc_start: 0.6017 (tpt) cc_final: 0.5694 (tpt) outliers start: 37 outliers final: 34 residues processed: 370 average time/residue: 0.3778 time to fit residues: 203.4540 Evaluate side-chains 372 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 337 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 83 HIS 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 56 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 119 THR 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 74 THR 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 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 69 ASP Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain P residue 75 ILE 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 R residue 88 ILE Chi-restraints excluded: chain S residue 66 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 162 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.071008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.055570 restraints weight = 363820.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.057371 restraints weight = 194663.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.058506 restraints weight = 130826.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.059201 restraints weight = 101697.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.059692 restraints weight = 87206.082| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.6724 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= 0.179 Angle : 0.654 7.633 34840 Z= 0.417 Chirality : 0.041 0.200 3964 Planarity : 0.005 0.069 2575 Dihedral : 30.593 118.781 7431 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.25 % Allowed : 26.02 % Favored : 70.73 % 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: 1.19 (0.21), residues: 1456 helix: 1.46 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -0.96 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 100 TYR 0.027 0.002 TYR F 99 PHE 0.016 0.002 PHE E 79 HIS 0.006 0.001 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.18 (24119) covalent geometry : angle 0.65402 / 0.42 (34840) hydrogen bonds : bond 0.06350 / 4.18 ( 1439) hydrogen bonds : angle 3.70229 / 2.71 ( 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 373 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 333 time to evaluate : 0.858 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: 0.8304 (mmm) cc_final: 0.8091 (mmp) REVERT: C 58 TYR cc_start: 0.7526 (t80) cc_final: 0.6612 (t80) REVERT: C 62 GLU cc_start: 0.8622 (mm-30) cc_final: 0.7834 (mm-30) REVERT: C 65 GLU cc_start: 0.7557 (tp30) cc_final: 0.7089 (tm-30) REVERT: F 74 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8941 (p) REVERT: G 62 GLU cc_start: 0.9597 (tp30) cc_final: 0.9316 (tp30) REVERT: H 60 MET cc_start: 0.6704 (tpp) cc_final: 0.6452 (tpp) REVERT: M 85 MET cc_start: 0.8836 (mmm) cc_final: 0.8532 (mmt) REVERT: O 96 GLN cc_start: 0.9605 (tt0) cc_final: 0.9387 (tt0) REVERT: Q 37 ARG cc_start: 0.8575 (mtm-85) cc_final: 0.7772 (mmp80) REVERT: R 58 TYR cc_start: 0.7699 (t80) cc_final: 0.7217 (t80) REVERT: R 62 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8594 (mm-30) outliers start: 40 outliers final: 32 residues processed: 355 average time/residue: 0.3865 time to fit residues: 200.4531 Evaluate side-chains 358 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 325 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 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 56 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 74 THR 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 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 69 ASP Chi-restraints excluded: chain O residue 83 HIS Chi-restraints excluded: chain O residue 101 LEU Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain P residue 75 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 63 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 186 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.068101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.052436 restraints weight = 377161.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.054323 restraints weight = 190866.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.055525 restraints weight = 124413.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.056290 restraints weight = 94700.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.056746 restraints weight = 79874.969| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.7297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24119 Z= 0.243 Angle : 0.714 8.952 34840 Z= 0.446 Chirality : 0.042 0.223 3964 Planarity : 0.006 0.100 2575 Dihedral : 30.730 119.293 7431 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.74 % Allowed : 25.93 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.20), residues: 1456 helix: 0.83 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -1.32 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 100 TYR 0.017 0.002 TYR H 41 PHE 0.020 0.003 PHE A 105 HIS 0.008 0.002 HIS Q 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.24 (24119) covalent geometry : angle 0.71375 / 0.45 (34840) hydrogen bonds : bond 0.08614 / 5.70 ( 1439) hydrogen bonds : angle 4.15280 / 3.02 ( 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 364 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 318 time to evaluate : 0.752 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: C 58 TYR cc_start: 0.7573 (t80) cc_final: 0.6574 (t80) REVERT: C 62 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7853 (mm-30) REVERT: C 65 GLU cc_start: 0.7399 (tp30) cc_final: 0.6975 (tm-30) REVERT: D 63 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6865 (mmm) REVERT: F 74 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8937 (p) REVERT: H 60 MET cc_start: 0.6732 (tpp) cc_final: 0.6400 (tpp) REVERT: M 85 MET cc_start: 0.8751 (mmm) cc_final: 0.8459 (mmt) REVERT: P 63 ILE cc_start: 0.6422 (mm) cc_final: 0.6192 (mm) REVERT: P 80 LYS cc_start: 0.8714 (tptp) cc_final: 0.8420 (tptp) REVERT: R 58 TYR cc_start: 0.7581 (t80) cc_final: 0.7046 (t80) REVERT: R 62 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8524 (mm-30) outliers start: 46 outliers final: 40 residues processed: 340 average time/residue: 0.3703 time to fit residues: 185.0453 Evaluate side-chains 350 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 308 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 D residue 63 MET 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 56 GLN Chi-restraints excluded: chain E residue 74 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 69 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 53 THR 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 46 LEU 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 O residue 103 LEU Chi-restraints excluded: chain P residue 111 CYS Chi-restraints excluded: chain P residue 121 MET Chi-restraints excluded: chain Q residue 67 ILE 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 R residue 80 ILE Chi-restraints excluded: chain R residue 108 VAL 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 132 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 182 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 39 HIS ** 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 = 0.4083 r_free = 0.4083 target = 0.069756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.053968 restraints weight = 369347.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.055908 restraints weight = 185003.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.057146 restraints weight = 119905.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.057926 restraints weight = 90988.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.058385 restraints weight = 76765.887| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.7348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24119 Z= 0.162 Angle : 0.668 7.582 34840 Z= 0.421 Chirality : 0.042 0.192 3964 Planarity : 0.005 0.073 2575 Dihedral : 30.752 119.934 7431 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.68 % Allowed : 27.32 % Favored : 70.00 % 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: 1.07 (0.21), residues: 1456 helix: 1.43 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -1.17 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 100 TYR 0.018 0.002 TYR A 55 PHE 0.019 0.002 PHE D 66 HIS 0.010 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.16 (24119) covalent geometry : angle 0.66831 / 0.42 (34840) hydrogen bonds : bond 0.06051 / 3.98 ( 1439) hydrogen bonds : angle 3.68973 / 2.69 ( 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 365 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 0.842 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: C 58 TYR cc_start: 0.7428 (t80) cc_final: 0.6406 (t80) REVERT: C 62 GLU cc_start: 0.8622 (mm-30) cc_final: 0.7821 (mm-30) REVERT: C 65 GLU cc_start: 0.7351 (tp30) cc_final: 0.6966 (tm-30) REVERT: F 74 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8906 (p) REVERT: G 62 GLU cc_start: 0.9555 (tp30) cc_final: 0.9274 (tp30) REVERT: L 56 GLN cc_start: 0.8960 (mt0) cc_final: 0.8624 (mm110) REVERT: M 85 MET cc_start: 0.8680 (mmm) cc_final: 0.8327 (mmt) REVERT: P 95 GLU cc_start: 0.8313 (tt0) cc_final: 0.8077 (tt0) REVERT: R 58 TYR cc_start: 0.7532 (t80) cc_final: 0.6961 (t80) REVERT: R 62 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8480 (mm-30) outliers start: 33 outliers final: 32 residues processed: 349 average time/residue: 0.3971 time to fit residues: 203.5886 Evaluate side-chains 355 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 322 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 90 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 119 THR 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 74 THR 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 46 LEU 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 O residue 103 LEU Chi-restraints excluded: chain P residue 121 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 50 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 73 optimal weight: 30.0000 chunk 140 optimal weight: 3.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.069138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.053161 restraints weight = 366679.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.055079 restraints weight = 185329.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.056313 restraints weight = 120713.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.057081 restraints weight = 91966.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.057593 restraints weight = 77697.319| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.7480 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= 0.181 Angle : 0.670 7.290 34840 Z= 0.422 Chirality : 0.041 0.199 3964 Planarity : 0.005 0.078 2575 Dihedral : 30.706 119.602 7431 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.76 % Allowed : 27.15 % Favored : 70.08 % 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: 1.06 (0.21), residues: 1456 helix: 1.43 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -1.20 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 100 TYR 0.021 0.002 TYR O 84 PHE 0.014 0.002 PHE Q 62 HIS 0.007 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.18 (24119) covalent geometry : angle 0.66963 / 0.42 (34840) hydrogen bonds : bond 0.06435 / 4.25 ( 1439) hydrogen bonds : angle 3.78144 / 2.76 ( 3613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7784.49 seconds wall clock time: 133 minutes 0.90 seconds (7980.90 seconds total)