Starting phenix.real_space_refine on Sun Feb 8 05:24:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mll_48375/02_2026/9mll_48375.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mll_48375/02_2026/9mll_48375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mll_48375/02_2026/9mll_48375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mll_48375/02_2026/9mll_48375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mll_48375/02_2026/9mll_48375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mll_48375/02_2026/9mll_48375.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 530 5.49 5 S 28 5.16 5 C 12580 2.51 5 N 4243 2.21 5 O 5258 1.98 5 H 18340 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 6.97, per 1000 atoms: 0.17 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: 3.80 Conformation dependent library (CDL) restraints added in 982.0 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: 8.01 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 78 removed outlier: 3.557A pdb=" N PHE A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.894A pdb=" N VAL A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.529A pdb=" N LEU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.047A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP B 69 " --> pdb=" O ASN B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 removed outlier: 3.633A pdb=" N VAL B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.377A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 69 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.645A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 removed outlier: 3.725A pdb=" N ASN D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.722A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.539A pdb=" N GLN E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 removed outlier: 3.685A pdb=" N VAL E 90 " --> pdb=" O GLN E 86 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.695A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 78 removed outlier: 3.955A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 95 removed outlier: 3.562A pdb=" N VAL F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.532A pdb=" N VAL G 31 " --> pdb=" O PRO G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 74 removed outlier: 3.592A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 removed outlier: 3.648A pdb=" N LEU G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 removed outlier: 3.533A pdb=" N LYS G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 56 through 85 removed outlier: 3.898A pdb=" N ASN H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 123 removed outlier: 3.799A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 58 Processing helix chain 'L' and resid 64 through 80 removed outlier: 4.189A pdb=" N GLN L 77 " --> pdb=" O ARG L 73 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP L 78 " --> pdb=" O GLU L 74 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE L 79 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 115 removed outlier: 3.860A pdb=" N VAL L 90 " --> pdb=" O GLN L 86 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET L 91 " --> pdb=" O SER L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 132 Processing helix chain 'M' and resid 31 through 40 Processing helix chain 'M' and resid 50 through 77 removed outlier: 4.070A pdb=" N GLU M 54 " --> pdb=" O LEU M 50 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 94 removed outlier: 3.724A pdb=" N VAL M 87 " --> pdb=" O THR M 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 23 Processing helix chain 'N' and resid 27 through 38 Processing helix chain 'N' and resid 46 through 74 removed outlier: 4.422A pdb=" N VAL N 50 " --> pdb=" O ALA N 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR N 51 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU N 66 " --> pdb=" O GLU N 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN N 69 " --> pdb=" O GLU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.537A pdb=" N LEU N 84 " --> pdb=" O ILE N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 98 Processing helix chain 'N' and resid 113 through 117 removed outlier: 3.503A pdb=" N LEU N 117 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 50 removed outlier: 3.593A pdb=" N GLN O 48 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL O 49 " --> pdb=" O VAL O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 85 removed outlier: 3.716A pdb=" N ASN O 68 " --> pdb=" O ASN O 64 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 103 Processing helix chain 'O' and resid 104 through 123 Processing helix chain 'P' and resid 45 through 58 removed outlier: 3.657A pdb=" N ARG P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS P 57 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER P 58 " --> pdb=" O ARG P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 80 removed outlier: 4.314A pdb=" N ASP P 78 " --> pdb=" O GLU P 74 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 115 removed outlier: 3.755A pdb=" N VAL P 90 " --> pdb=" O GLN P 86 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET P 91 " --> pdb=" O SER P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 133 removed outlier: 3.637A pdb=" N ILE P 125 " --> pdb=" O MET P 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.602A pdb=" N ILE Q 30 " --> pdb=" O ILE Q 27 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 42 Processing helix chain 'Q' and resid 50 through 77 removed outlier: 3.917A pdb=" N GLU Q 54 " --> pdb=" O LEU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 95 removed outlier: 3.538A pdb=" N VAL Q 87 " --> pdb=" O THR Q 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 23 Processing helix chain 'R' and resid 27 through 37 removed outlier: 3.568A pdb=" N VAL R 31 " --> pdb=" O PRO R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 74 removed outlier: 3.695A pdb=" N LEU R 66 " --> pdb=" O GLU R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 89 removed outlier: 3.592A pdb=" N LEU R 84 " --> pdb=" O ILE R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 98 removed outlier: 3.564A pdb=" N LYS R 96 " --> pdb=" O GLU R 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 50 Processing helix chain 'S' and resid 56 through 85 removed outlier: 3.889A pdb=" N ASN S 85 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 103 Processing helix chain 'S' and resid 104 through 124 removed outlier: 3.552A pdb=" N LYS S 109 " --> pdb=" O GLY S 105 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N HIS S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.680A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.267A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.914A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 7.086A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.323A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB1, first strand: chain 'L' and resid 84 through 85 removed outlier: 6.655A pdb=" N ARG L 84 " --> pdb=" O VAL M 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'M' and resid 98 through 99 Processing sheet with id=AB3, first strand: chain 'N' and resid 43 through 44 removed outlier: 7.260A pdb=" N ARG N 43 " --> pdb=" O ILE O 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'N' and resid 78 through 79 Processing sheet with id=AB5, first strand: chain 'N' and resid 102 through 103 removed outlier: 6.969A pdb=" N THR N 102 " --> pdb=" O TYR Q 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'P' and resid 84 through 85 removed outlier: 7.050A pdb=" N ARG P 84 " --> pdb=" O VAL Q 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'P' and resid 119 through 120 Processing sheet with id=AB8, first strand: chain 'R' and resid 43 through 44 removed outlier: 7.329A pdb=" N ARG R 43 " --> pdb=" O ILE S 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'R' and resid 78 through 79 759 hydrogen bonds defined for protein. 2253 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 680 hydrogen bonds 1360 hydrogen bond angles 0 basepair planarities 264 basepair parallelities 450 stacking parallelities Total time for adding SS restraints: 10.03 Time building geometry restraints manager: 5.19 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 1.525 1.565 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C3' DT X 43 " pdb=" C2' DT X 43 " ideal model delta sigma weight residual 1.525 1.563 -0.038 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C4' DT X 43 " pdb=" O4' DT X 43 " ideal model delta sigma weight residual 1.450 1.414 0.036 2.00e-02 2.50e+03 3.17e+00 bond pdb=" C4' DT I 43 " pdb=" O4' DT I 43 " ideal model delta sigma weight residual 1.450 1.415 0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" CB ILE A 52 " pdb=" CG2 ILE A 52 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.47e+00 ... (remaining 42454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 67241 1.29 - 2.58: 8639 2.58 - 3.87: 916 3.87 - 5.16: 144 5.16 - 6.45: 19 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 108.40 114.73 -6.33 1.50e+00 4.44e-01 1.78e+01 angle pdb=" C2' DT I 43 " pdb=" C1' DT I 43 " pdb=" N1 DT I 43 " ideal model delta sigma weight residual 113.50 119.71 -6.21 1.50e+00 4.44e-01 1.71e+01 angle pdb=" C2' DT X 43 " pdb=" C1' DT X 43 " pdb=" N1 DT X 43 " ideal model delta sigma weight residual 113.50 119.56 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C2' DC I 7 " pdb=" C1' DC I 7 " pdb=" N1 DC I 7 " ideal model delta sigma weight residual 113.50 119.37 -5.87 1.50e+00 4.44e-01 1.53e+01 angle pdb=" O4' DA I -54 " pdb=" C1' DA I -54 " pdb=" N9 DA I -54 " ideal model delta sigma weight residual 108.40 102.70 5.70 1.50e+00 4.44e-01 1.44e+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 - 0.049: 2695 0.049 - 0.097: 956 0.097 - 0.146: 239 0.146 - 0.194: 56 0.194 - 0.243: 18 Chirality restraints: 3964 Sorted by residual: chirality pdb=" C4' DG X -7 " pdb=" C5' DG X -7 " pdb=" O4' DG X -7 " pdb=" C3' DG X -7 " both_signs ideal model delta sigma weight residual False -2.53 -2.28 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" C1' DC I 66 " pdb=" O4' DC I 66 " pdb=" C2' DC I 66 " pdb=" N1 DC I 66 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C4' DC I 21 " pdb=" C5' DC I 21 " pdb=" O4' DC I 21 " pdb=" C3' DC I 21 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 3961 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 7 " 0.060 2.00e-02 2.50e+03 3.21e-02 2.84e+01 pdb=" N1 DC I 7 " -0.081 2.00e-02 2.50e+03 pdb=" C2 DC I 7 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DC I 7 " -0.014 2.00e-02 2.50e+03 pdb=" N3 DC I 7 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC I 7 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC I 7 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DC I 7 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 7 " -0.008 2.00e-02 2.50e+03 pdb=" H5 DC I 7 " 0.005 2.00e-02 2.50e+03 pdb=" H6 DC I 7 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC X -21 " 0.059 2.00e-02 2.50e+03 3.21e-02 2.84e+01 pdb=" N1 DC X -21 " -0.081 2.00e-02 2.50e+03 pdb=" C2 DC X -21 " 0.021 2.00e-02 2.50e+03 pdb=" O2 DC X -21 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC X -21 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC X -21 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC X -21 " 0.018 2.00e-02 2.50e+03 pdb=" C5 DC X -21 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC X -21 " -0.018 2.00e-02 2.50e+03 pdb=" H5 DC X -21 " 0.010 2.00e-02 2.50e+03 pdb=" H6 DC X -21 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -12 " 0.042 2.00e-02 2.50e+03 3.14e-02 2.71e+01 pdb=" N1 DC I -12 " -0.085 2.00e-02 2.50e+03 pdb=" C2 DC I -12 " 0.039 2.00e-02 2.50e+03 pdb=" O2 DC I -12 " -0.009 2.00e-02 2.50e+03 pdb=" N3 DC I -12 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I -12 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I -12 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DC I -12 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC I -12 " -0.000 2.00e-02 2.50e+03 pdb=" H5 DC I -12 " 0.007 2.00e-02 2.50e+03 pdb=" H6 DC I -12 " 0.003 2.00e-02 2.50e+03 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1101 2.15 - 2.76: 64363 2.76 - 3.37: 105568 3.37 - 3.99: 142232 3.99 - 4.60: 220119 Nonbonded interactions: 533383 Sorted by model distance: nonbonded pdb=" OE1 GLU L 51 " pdb=" HE ARG M 40 " model vdw 1.534 2.450 nonbonded pdb=" O ILE A 63 " pdb="HE22 GLN A 94 " model vdw 1.541 2.450 nonbonded pdb=" OD2 ASP E 107 " pdb="HH11 ARG E 132 " model vdw 1.557 2.450 nonbonded pdb=" H GLY B 49 " pdb=" OP1 DC J 7 " model vdw 1.592 2.450 nonbonded pdb=" OD2 ASP L 107 " pdb="HH11 ARG L 132 " model vdw 1.593 2.450 ... (remaining 533378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 42 through 134) selection = chain 'E' selection = (chain 'L' and resid 42 through 134) selection = (chain 'P' and resid 42 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 103) selection = (chain 'M' and resid 25 through 103) selection = chain 'Q' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = (chain 'G' and resid 16 through 118) selection = chain 'N' selection = (chain 'R' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 35 through 123) selection = chain 'H' selection = chain 'O' selection = (chain 'S' and resid 35 through 123) } ncs_group { reference = (chain 'I' and resid -67 through 58) selection = (chain 'X' and resid -67 through 58) } ncs_group { reference = (chain 'J' and resid -58 through 67) selection = (chain 'Y' and resid -58 through 67) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 43.740 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5208 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24119 Z= 0.244 Angle : 0.939 6.446 34840 Z= 0.602 Chirality : 0.055 0.243 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 covalent geometry : bond 0.00515 (24119) covalent geometry : angle 0.93886 (34840) hydrogen bonds : bond 0.10468 ( 1439) hydrogen bonds : angle 4.29727 ( 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 : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 ILE cc_start: 0.7701 (mm) cc_final: 0.7327 (mm) outliers start: 10 outliers final: 4 residues processed: 633 average time/residue: 0.4751 time to fit residues: 410.0670 Evaluate side-chains 418 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 414 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 94 GLN D 85 ASN D 96 GLN E 86 GLN G 39 HIS L 86 GLN M 94 GLN P 77 GLN P 86 GLN Q 26 ASN R 25 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.078430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.063073 restraints weight = 314180.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.065165 restraints weight = 165151.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.066544 restraints weight = 106662.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.067445 restraints weight = 78995.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.068073 restraints weight = 64661.688| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24119 Z= 0.208 Angle : 0.692 6.505 34840 Z= 0.423 Chirality : 0.041 0.142 3964 Planarity : 0.005 0.051 2575 Dihedral : 29.788 114.919 7440 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.36 % Allowed : 20.49 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1456 helix: 1.42 (0.15), residues: 1040 sheet: None (None), residues: 0 loop : -0.26 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 130 TYR 0.019 0.002 TYR Q 73 PHE 0.014 0.002 PHE O 66 HIS 0.005 0.001 HIS Q 76 Details of bonding type rmsd covalent geometry : bond 0.00438 (24119) covalent geometry : angle 0.69228 (34840) hydrogen bonds : bond 0.06177 ( 1439) hydrogen bonds : angle 3.59228 ( 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 472 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 443 time to evaluate : 0.873 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: A 80 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8676 (mptt) REVERT: C 58 TYR cc_start: 0.7365 (t80) cc_final: 0.6907 (t80) REVERT: C 62 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8150 (mm-30) REVERT: E 79 PHE cc_start: 0.6569 (m-10) cc_final: 0.6308 (m-10) REVERT: F 63 LEU cc_start: 0.9770 (mt) cc_final: 0.9522 (mt) REVERT: F 64 GLU cc_start: 0.9515 (mt-10) cc_final: 0.9288 (mt-10) REVERT: G 62 GLU cc_start: 0.9519 (tp30) cc_final: 0.9179 (tp30) REVERT: G 69 ASN cc_start: 0.8277 (t0) cc_final: 0.7885 (t0) REVERT: L 107 ASP cc_start: 0.9037 (m-30) cc_final: 0.8817 (m-30) REVERT: M 72 THR cc_start: 0.9351 (m) cc_final: 0.9089 (p) REVERT: N 42 GLU cc_start: 0.6755 (pm20) cc_final: 0.6415 (pm20) REVERT: N 43 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7743 (mtp85) REVERT: O 96 GLN cc_start: 0.9523 (tt0) cc_final: 0.9322 (tt0) REVERT: P 80 LYS cc_start: 0.9068 (tptp) cc_final: 0.8829 (tptp) REVERT: R 65 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7218 (tm-30) REVERT: R 69 ASN cc_start: 0.7597 (m-40) cc_final: 0.7132 (m110) outliers start: 29 outliers final: 18 residues processed: 453 average time/residue: 0.4181 time to fit residues: 265.4998 Evaluate side-chains 414 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 396 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 E residue 59 THR Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 69 ASP 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 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain R residue 35 LEU 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: 0.7980 chunk 94 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 181 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 25 GLN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4092 r_free = 0.4092 target = 0.070601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.055255 restraints weight = 369478.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.057053 restraints weight = 198772.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.058210 restraints weight = 133895.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.058949 restraints weight = 103617.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.059400 restraints weight = 88330.838| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 24119 Z= 0.264 Angle : 0.730 7.169 34840 Z= 0.443 Chirality : 0.044 0.180 3964 Planarity : 0.006 0.079 2575 Dihedral : 30.106 105.060 7431 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.15 % Allowed : 20.16 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1456 helix: 1.05 (0.15), residues: 1055 sheet: None (None), residues: 0 loop : -0.56 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 79 TYR 0.022 0.002 TYR O 84 PHE 0.015 0.002 PHE S 71 HIS 0.007 0.002 HIS N 83 Details of bonding type rmsd covalent geometry : bond 0.00554 (24119) covalent geometry : angle 0.72974 (34840) hydrogen bonds : bond 0.07768 ( 1439) hydrogen bonds : angle 4.06224 ( 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 437 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 386 time to evaluate : 0.681 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: A 134 GLU cc_start: 0.8220 (mp0) cc_final: 0.7130 (pm20) REVERT: C 42 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: C 58 TYR cc_start: 0.7634 (t80) cc_final: 0.6862 (t80) REVERT: C 62 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8019 (mm-30) REVERT: C 65 GLU cc_start: 0.7892 (tp30) cc_final: 0.7691 (tp30) REVERT: D 66 PHE cc_start: 0.7225 (t80) cc_final: 0.6914 (t80) REVERT: F 54 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8547 (mp0) REVERT: F 64 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9277 (mt-10) REVERT: G 69 ASN cc_start: 0.8203 (t0) cc_final: 0.8003 (t0) REVERT: M 28 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8787 (pm20) REVERT: O 60 MET cc_start: 0.7686 (tmm) cc_final: 0.7340 (tpt) REVERT: P 55 TYR cc_start: 0.8870 (m-80) cc_final: 0.8299 (m-80) REVERT: P 80 LYS cc_start: 0.9034 (tptp) cc_final: 0.8802 (tptp) REVERT: R 65 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7220 (tm-30) REVERT: R 69 ASN cc_start: 0.7838 (m-40) cc_final: 0.7266 (m110) outliers start: 51 outliers final: 40 residues processed: 408 average time/residue: 0.3737 time to fit residues: 217.4721 Evaluate side-chains 388 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 347 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 42 GLU 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 E residue 119 THR Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 24 ARG 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 G residue 50 VAL Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain P residue 106 GLU Chi-restraints excluded: chain Q residue 67 ILE Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 93 ARG Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 72 GLU Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain S residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 81 optimal weight: 10.0000 chunk 18 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 166 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 ASN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.072477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.057365 restraints weight = 365140.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.059233 restraints weight = 193608.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.060441 restraints weight = 129414.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.061202 restraints weight = 99414.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.061740 restraints weight = 84335.309| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24119 Z= 0.174 Angle : 0.649 6.007 34840 Z= 0.397 Chirality : 0.038 0.141 3964 Planarity : 0.004 0.042 2575 Dihedral : 30.029 105.577 7431 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.25 % Allowed : 21.79 % Favored : 74.96 % 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: 1.70 (0.21), residues: 1456 helix: 1.76 (0.15), residues: 1053 sheet: None (None), residues: 0 loop : -0.51 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 36 TYR 0.023 0.001 TYR A 55 PHE 0.019 0.001 PHE H 66 HIS 0.009 0.001 HIS R 32 Details of bonding type rmsd covalent geometry : bond 0.00368 (24119) covalent geometry : angle 0.64907 (34840) hydrogen bonds : bond 0.04748 ( 1439) hydrogen bonds : angle 3.41326 ( 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 415 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 375 time to evaluate : 0.601 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: C 93 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7843 (tt0) REVERT: D 60 MET cc_start: 0.7154 (tpp) cc_final: 0.6852 (tpp) REVERT: D 66 PHE cc_start: 0.6974 (t80) cc_final: 0.6735 (t80) REVERT: G 69 ASN cc_start: 0.8341 (t0) cc_final: 0.8090 (t0) REVERT: M 28 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8733 (pm20) REVERT: N 57 GLU cc_start: 0.9158 (tt0) cc_final: 0.8475 (tt0) REVERT: N 111 ASN cc_start: 0.8895 (t0) cc_final: 0.8107 (m110) REVERT: P 55 TYR cc_start: 0.8804 (m-80) cc_final: 0.7981 (m-80) REVERT: P 80 LYS cc_start: 0.9049 (tptp) cc_final: 0.8844 (tptp) REVERT: Q 37 ARG cc_start: 0.8510 (mtm-85) cc_final: 0.7851 (mmp80) REVERT: R 65 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7278 (tm-30) REVERT: R 69 ASN cc_start: 0.7911 (m-40) cc_final: 0.7239 (m110) outliers start: 40 outliers final: 36 residues processed: 392 average time/residue: 0.3743 time to fit residues: 211.1053 Evaluate side-chains 380 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 344 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 55 ILE 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 59 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain 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 103 LEU Chi-restraints excluded: chain P residue 106 GLU Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 36 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 44 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.068724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.053996 restraints weight = 379973.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.055704 restraints weight = 205517.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.056803 restraints weight = 139936.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.057509 restraints weight = 108478.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.058018 restraints weight = 92448.798| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24119 Z= 0.251 Angle : 0.678 6.563 34840 Z= 0.416 Chirality : 0.043 0.148 3964 Planarity : 0.005 0.044 2575 Dihedral : 30.120 103.137 7431 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.15 % Allowed : 23.41 % Favored : 72.44 % 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: 1.33 (0.21), residues: 1456 helix: 1.50 (0.15), residues: 1055 sheet: None (None), residues: 0 loop : -0.69 (0.27), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 100 TYR 0.015 0.002 TYR R 40 PHE 0.015 0.002 PHE H 66 HIS 0.007 0.001 HIS Q 76 Details of bonding type rmsd covalent geometry : bond 0.00519 (24119) covalent geometry : angle 0.67834 (34840) hydrogen bonds : bond 0.07248 ( 1439) hydrogen bonds : angle 3.80750 ( 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 388 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 0.732 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: C 65 GLU cc_start: 0.8262 (tp30) cc_final: 0.7738 (tm-30) REVERT: D 106 GLU cc_start: 0.8975 (mp0) cc_final: 0.8699 (pm20) REVERT: F 54 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8520 (mp0) REVERT: H 60 MET cc_start: 0.6627 (tpp) cc_final: 0.6210 (tpp) REVERT: L 56 GLN cc_start: 0.9077 (mt0) cc_final: 0.8497 (mm110) REVERT: M 28 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8774 (pm20) REVERT: R 65 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7373 (tm-30) REVERT: R 69 ASN cc_start: 0.7953 (m-40) cc_final: 0.7288 (m110) outliers start: 51 outliers final: 42 residues processed: 357 average time/residue: 0.3875 time to fit residues: 198.4953 Evaluate side-chains 364 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 322 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 55 ILE 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 47 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 50 VAL 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 L residue 119 THR Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 42 GLU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 95 ILE Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 66 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 156 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 74 ASN ** 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 = 0.4008 r_free = 0.4008 target = 0.065547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.050235 restraints weight = 386339.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.052015 restraints weight = 191985.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.053155 restraints weight = 124853.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.053888 restraints weight = 95538.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.054338 restraints weight = 80977.284| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24119 Z= 0.249 Angle : 0.693 6.129 34840 Z= 0.424 Chirality : 0.043 0.149 3964 Planarity : 0.005 0.068 2575 Dihedral : 30.535 97.071 7431 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.63 % Allowed : 22.93 % Favored : 72.44 % 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: 0.86 (0.21), residues: 1456 helix: 1.17 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -0.95 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 100 TYR 0.025 0.002 TYR A 55 PHE 0.020 0.003 PHE E 79 HIS 0.007 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00513 (24119) covalent geometry : angle 0.69292 (34840) hydrogen bonds : bond 0.07197 ( 1439) hydrogen bonds : angle 3.97623 ( 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 379 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 322 time to evaluate : 0.787 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: C 42 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8125 (pm20) REVERT: C 65 GLU cc_start: 0.7848 (tp30) cc_final: 0.7458 (tm-30) REVERT: H 60 MET cc_start: 0.6921 (tpp) cc_final: 0.6470 (tpp) REVERT: P 46 THR cc_start: 0.7549 (m) cc_final: 0.7294 (p) REVERT: P 47 VAL cc_start: 0.8044 (t) cc_final: 0.7833 (t) outliers start: 57 outliers final: 46 residues processed: 350 average time/residue: 0.3857 time to fit residues: 194.6919 Evaluate side-chains 346 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 38 TYR Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain L residue 77 GLN Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 116 optimal weight: 0.0470 chunk 136 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.065094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.049926 restraints weight = 383545.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.051727 restraints weight = 191260.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.052874 restraints weight = 124513.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.053600 restraints weight = 94940.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.054078 restraints weight = 80255.810| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.8977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24119 Z= 0.231 Angle : 0.676 7.295 34840 Z= 0.414 Chirality : 0.041 0.152 3964 Planarity : 0.005 0.090 2575 Dihedral : 30.512 93.549 7431 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.58 % Allowed : 25.85 % Favored : 70.57 % 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: 0.99 (0.21), residues: 1456 helix: 1.34 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -1.12 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 100 TYR 0.017 0.002 TYR H 41 PHE 0.013 0.002 PHE O 66 HIS 0.006 0.001 HIS Q 76 Details of bonding type rmsd covalent geometry : bond 0.00476 (24119) covalent geometry : angle 0.67579 (34840) hydrogen bonds : bond 0.06909 ( 1439) hydrogen bonds : angle 3.83616 ( 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 357 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 313 time to evaluate : 0.824 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: C 62 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7950 (mm-30) REVERT: C 65 GLU cc_start: 0.7720 (tp30) cc_final: 0.7352 (tm-30) REVERT: F 54 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8751 (mp0) REVERT: G 58 TYR cc_start: 0.8970 (t80) cc_final: 0.8756 (t80) REVERT: H 96 GLN cc_start: 0.9431 (tt0) cc_final: 0.9051 (tp40) REVERT: P 46 THR cc_start: 0.7592 (m) cc_final: 0.7327 (p) REVERT: Q 60 LYS cc_start: 0.9555 (tptm) cc_final: 0.9135 (tptm) REVERT: Q 64 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8906 (mt-10) outliers start: 44 outliers final: 37 residues processed: 333 average time/residue: 0.3858 time to fit residues: 185.6918 Evaluate side-chains 340 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 303 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 66 PHE 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 59 THR 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 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain H residue 69 ASP 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 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 103 LEU Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 59 LEU 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: 10.0000 chunk 163 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.065876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.050728 restraints weight = 381068.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.052550 restraints weight = 189173.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.053708 restraints weight = 122759.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.054431 restraints weight = 93638.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.054921 restraints weight = 79369.471| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.9226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24119 Z= 0.196 Angle : 0.656 6.804 34840 Z= 0.400 Chirality : 0.039 0.145 3964 Planarity : 0.005 0.061 2575 Dihedral : 30.447 93.791 7431 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.93 % Allowed : 26.50 % Favored : 70.57 % 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: 1.36 (0.21), residues: 1456 helix: 1.65 (0.16), residues: 1055 sheet: None (None), residues: 0 loop : -1.13 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 68 TYR 0.015 0.001 TYR H 41 PHE 0.017 0.002 PHE H 66 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00410 (24119) covalent geometry : angle 0.65563 (34840) hydrogen bonds : bond 0.05515 ( 1439) hydrogen bonds : angle 3.56582 ( 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 355 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 319 time to evaluate : 0.764 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: A 82 ASP cc_start: 0.8908 (m-30) cc_final: 0.8464 (m-30) REVERT: A 121 MET cc_start: 0.6183 (mtt) cc_final: 0.5943 (mtt) REVERT: C 58 TYR cc_start: 0.7772 (t80) cc_final: 0.6773 (t80) REVERT: C 62 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8012 (mm-30) REVERT: C 65 GLU cc_start: 0.7708 (tp30) cc_final: 0.7305 (tm-30) REVERT: D 106 GLU cc_start: 0.8755 (pm20) cc_final: 0.8536 (pm20) REVERT: F 54 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8738 (mp0) REVERT: G 73 ASP cc_start: 0.8785 (t0) cc_final: 0.8544 (m-30) REVERT: P 46 THR cc_start: 0.7560 (m) cc_final: 0.7289 (p) REVERT: P 60 GLU cc_start: 0.7341 (pm20) cc_final: 0.7131 (pm20) REVERT: Q 60 LYS cc_start: 0.9595 (tptm) cc_final: 0.9180 (tptm) REVERT: Q 64 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8911 (mt-10) REVERT: R 42 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7348 (pm20) outliers start: 36 outliers final: 29 residues processed: 337 average time/residue: 0.3845 time to fit residues: 187.8344 Evaluate side-chains 328 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 298 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 66 PHE 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 74 GLU Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 69 ASP 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 64 GLU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 42 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 46 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: 0.9980 chunk 155 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.063944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.048768 restraints weight = 387531.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.050510 restraints weight = 193710.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.051609 restraints weight = 126675.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.052269 restraints weight = 97241.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.052732 restraints weight = 83152.507| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.9628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24119 Z= 0.232 Angle : 0.678 6.807 34840 Z= 0.413 Chirality : 0.041 0.149 3964 Planarity : 0.005 0.104 2575 Dihedral : 30.490 93.550 7431 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.17 % Allowed : 26.59 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1456 helix: 1.50 (0.16), residues: 1058 sheet: None (None), residues: 0 loop : -1.22 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 53 TYR 0.017 0.002 TYR H 41 PHE 0.014 0.002 PHE Q 101 HIS 0.005 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00481 (24119) covalent geometry : angle 0.67778 (34840) hydrogen bonds : bond 0.07035 ( 1439) hydrogen bonds : angle 3.75857 ( 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 344 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 305 time to evaluate : 0.861 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: C 62 GLU cc_start: 0.8583 (mm-30) cc_final: 0.7920 (mm-30) REVERT: C 65 GLU cc_start: 0.7659 (tp30) cc_final: 0.7306 (tm-30) REVERT: F 54 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8780 (mp0) REVERT: P 46 THR cc_start: 0.7745 (m) cc_final: 0.7464 (p) REVERT: P 60 GLU cc_start: 0.7333 (pm20) cc_final: 0.7108 (pm20) REVERT: R 42 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7375 (pm20) outliers start: 39 outliers final: 36 residues processed: 323 average time/residue: 0.3794 time to fit residues: 176.9558 Evaluate side-chains 330 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 69 ASP 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 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 42 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 132 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 159 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.063655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.048748 restraints weight = 385964.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.050495 restraints weight = 191520.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.051588 restraints weight = 124773.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.052262 restraints weight = 95710.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.052709 restraints weight = 81512.841| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.9961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24119 Z= 0.227 Angle : 0.682 7.040 34840 Z= 0.415 Chirality : 0.041 0.148 3964 Planarity : 0.005 0.095 2575 Dihedral : 30.578 91.157 7431 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.33 % Allowed : 26.75 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.21), residues: 1456 helix: 1.43 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.34 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 53 TYR 0.017 0.002 TYR S 84 PHE 0.013 0.002 PHE Q 101 HIS 0.006 0.001 HIS N 83 Details of bonding type rmsd covalent geometry : bond 0.00471 (24119) covalent geometry : angle 0.68248 (34840) hydrogen bonds : bond 0.06508 ( 1439) hydrogen bonds : angle 3.76760 ( 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 345 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 0.730 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: C 42 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8156 (pm20) REVERT: C 62 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7978 (mm-30) REVERT: C 65 GLU cc_start: 0.7673 (tp30) cc_final: 0.7364 (tm-30) REVERT: C 69 ASN cc_start: 0.7949 (m-40) cc_final: 0.7078 (m-40) REVERT: D 106 GLU cc_start: 0.8787 (pm20) cc_final: 0.8570 (pm20) REVERT: F 54 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8799 (mp0) REVERT: P 46 THR cc_start: 0.7768 (m) cc_final: 0.7489 (p) REVERT: P 60 GLU cc_start: 0.7425 (pm20) cc_final: 0.7215 (pm20) REVERT: R 42 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7287 (pm20) outliers start: 41 outliers final: 39 residues processed: 326 average time/residue: 0.3619 time to fit residues: 171.2069 Evaluate side-chains 334 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 293 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain F residue 21 LYS Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 69 ASP Chi-restraints excluded: chain H residue 107 LEU Chi-restraints excluded: chain L residue 46 THR Chi-restraints excluded: chain L residue 74 GLU Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 64 GLU Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 109 LYS Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 36 ARG Chi-restraints excluded: chain R residue 42 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 66 PHE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 THR 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: 10.0000 chunk 52 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.062027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.047258 restraints weight = 398801.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.048966 restraints weight = 198699.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.050049 restraints weight = 129341.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.050728 restraints weight = 99160.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.051130 restraints weight = 84262.423| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 1.0327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 24119 Z= 0.272 Angle : 0.710 9.281 34840 Z= 0.432 Chirality : 0.044 0.152 3964 Planarity : 0.006 0.100 2575 Dihedral : 30.711 90.267 7431 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.41 % Allowed : 27.07 % Favored : 69.51 % 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: 0.62 (0.21), residues: 1456 helix: 1.15 (0.15), residues: 1052 sheet: None (None), residues: 0 loop : -1.53 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 53 TYR 0.022 0.002 TYR S 84 PHE 0.017 0.002 PHE H 66 HIS 0.006 0.001 HIS M 76 Details of bonding type rmsd covalent geometry : bond 0.00563 (24119) covalent geometry : angle 0.71040 (34840) hydrogen bonds : bond 0.08221 ( 1439) hydrogen bonds : angle 4.03241 ( 3613) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7664.12 seconds wall clock time: 131 minutes 1.36 seconds (7861.36 seconds total)