Starting phenix.real_space_refine on Thu Aug 6 13:40:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pm0_71726/08_2026/9pm0_71726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pm0_71726/08_2026/9pm0_71726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pm0_71726/08_2026/9pm0_71726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pm0_71726/08_2026/9pm0_71726.map" model { file = "/net/cci-nas-00/data/ceres_data/9pm0_71726/08_2026/9pm0_71726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pm0_71726/08_2026/9pm0_71726.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 34 5.16 5 C 8888 2.51 5 N 2822 2.21 5 O 3566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15610 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "E" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "B" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "C" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "H" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "I" Number of atoms: 3056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3056 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3094 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Time building chain proxies: 3.82, per 1000 atoms: 0.24 Number of scatterers: 15610 At special positions: 0 Unit cell: (124.575, 127.05, 117.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 300 15.00 O 3566 8.00 N 2822 7.00 C 8888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.03 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 587.7 milliseconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 15 sheets defined 42.9% alpha, 11.6% beta 21 base pairs and 125 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 14 through 20 removed outlier: 4.061A pdb=" N LYS A 18 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 36 removed outlier: 4.033A pdb=" N MET A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 32 " --> pdb=" O MET A 28 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 71 removed outlier: 3.609A pdb=" N ALA A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 52 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.578A pdb=" N ILE A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.905A pdb=" N LEU A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.827A pdb=" N LEU A 114 " --> pdb=" O HIS A 110 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 115' Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.568A pdb=" N TYR E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE E 32 " --> pdb=" O MET E 28 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY E 35 " --> pdb=" O TYR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 71 removed outlier: 3.612A pdb=" N ALA E 51 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 52 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 53 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 56 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASP E 70 " --> pdb=" O ASN E 66 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 87 removed outlier: 3.596A pdb=" N ILE E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU E 82 " --> pdb=" O PRO E 78 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 84 " --> pdb=" O HIS E 80 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL E 85 " --> pdb=" O ILE E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.981A pdb=" N LEU E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 115 removed outlier: 3.874A pdb=" N LEU E 114 " --> pdb=" O HIS E 110 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 115' Processing helix chain 'B' and resid 39 through 50 removed outlier: 4.101A pdb=" N TYR B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 45 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 47 " --> pdb=" O TYR B 43 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 49 " --> pdb=" O VAL B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 85 removed outlier: 4.095A pdb=" N SER B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 67 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B 72 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.883A pdb=" N ILE B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B 100 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 125 removed outlier: 4.425A pdb=" N SER B 113 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 48 removed outlier: 4.412A pdb=" N TYR F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL F 45 " --> pdb=" O TYR F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 85 removed outlier: 3.567A pdb=" N MET F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER F 65 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE F 66 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL F 67 " --> pdb=" O MET F 63 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY F 76 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 101 removed outlier: 3.917A pdb=" N ILE F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 114 removed outlier: 4.114A pdb=" N SER F 113 " --> pdb=" O LYS F 109 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 109 through 114' Processing helix chain 'F' and resid 115 through 125 removed outlier: 3.680A pdb=" N VAL F 119 " --> pdb=" O GLY F 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 4.113A pdb=" N GLU C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 58 removed outlier: 3.592A pdb=" N LYS C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 80 removed outlier: 3.917A pdb=" N PHE C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 72 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 114 removed outlier: 3.568A pdb=" N VAL C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 92 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N CYS C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.866A pdb=" N ALA C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 51 removed outlier: 3.651A pdb=" N GLU G 51 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 58 removed outlier: 3.535A pdb=" N LYS G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 80 removed outlier: 3.852A pdb=" N PHE G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP G 78 " --> pdb=" O GLU G 74 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 114 removed outlier: 3.763A pdb=" N VAL G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 92 " --> pdb=" O SER G 88 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU G 101 " --> pdb=" O SER G 97 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP G 107 " --> pdb=" O ALA G 103 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 110 " --> pdb=" O GLU G 106 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS G 111 " --> pdb=" O ASP G 107 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA G 112 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 113 " --> pdb=" O ASN G 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS G 114 " --> pdb=" O LEU G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 123 No H-bonds generated for 'chain 'G' and resid 121 through 123' Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.896A pdb=" N ALA G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG G 129 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG G 130 " --> pdb=" O GLN G 126 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG G 132 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 43 removed outlier: 3.546A pdb=" N ARG D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG D 41 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 63 removed outlier: 4.122A pdb=" N ARG D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 60 " --> pdb=" O ARG D 56 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 3.641A pdb=" N THR D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 91 removed outlier: 4.378A pdb=" N VAL D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 43 removed outlier: 3.691A pdb=" N ARG H 36 " --> pdb=" O LYS H 32 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG H 41 " --> pdb=" O ARG H 37 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY H 42 " --> pdb=" O LEU H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 63 removed outlier: 4.310A pdb=" N ARG H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS H 60 " --> pdb=" O ARG H 56 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL H 61 " --> pdb=" O GLY H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 77 removed outlier: 3.562A pdb=" N VAL H 71 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA H 77 " --> pdb=" O TYR H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 95 removed outlier: 4.170A pdb=" N VAL H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ARG H 93 " --> pdb=" O TYR H 89 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLN H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 236 through 240 removed outlier: 3.878A pdb=" N SER M 240 " --> pdb=" O SER M 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 240 removed outlier: 3.876A pdb=" N SER N 240 " --> pdb=" O SER N 237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.444A pdb=" N ARG A 40 " --> pdb=" O ILE B 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 40 through 41 removed outlier: 6.480A pdb=" N ARG E 40 " --> pdb=" O ILE F 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.946A pdb=" N ARG C 84 " --> pdb=" O VAL D 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 84 through 85 removed outlier: 6.535A pdb=" N ARG G 84 " --> pdb=" O VAL H 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'M' and resid 24 through 25 removed outlier: 4.110A pdb=" N VAL M 38 " --> pdb=" O ILE M 94 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 94 " --> pdb=" O VAL M 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 64 through 68 removed outlier: 6.546A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR M 106 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR M 105 " --> pdb=" O THR M 121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR M 121 " --> pdb=" O TYR M 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 152 through 155 removed outlier: 4.681A pdb=" N GLN M 152 " --> pdb=" O SER M 174 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER M 174 " --> pdb=" O GLN M 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 159 through 161 removed outlier: 3.672A pdb=" N THR M 266 " --> pdb=" O GLU M 159 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL M 161 " --> pdb=" O THR M 266 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR M 243 " --> pdb=" O THR M 263 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL M 242 " --> pdb=" O GLN M 188 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE M 197 " --> pdb=" O TRP M 185 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR M 199 " --> pdb=" O LYS M 208 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS M 208 " --> pdb=" O TYR M 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 167 through 168 removed outlier: 3.717A pdb=" N VAL M 167 " --> pdb=" O LEU M 232 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU M 232 " --> pdb=" O VAL M 167 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR M 229 " --> pdb=" O THR M 220 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR M 220 " --> pdb=" O TYR M 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 24 through 25 removed outlier: 4.064A pdb=" N VAL N 38 " --> pdb=" O ILE N 94 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE N 94 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER N 91 " --> pdb=" O SER N 84 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER N 84 " --> pdb=" O SER N 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 64 through 68 removed outlier: 6.144A pdb=" N THR N 65 " --> pdb=" O GLN N 56 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN N 56 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE N 67 " --> pdb=" O TRP N 54 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP N 54 " --> pdb=" O ILE N 67 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR N 106 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR N 104 " --> pdb=" O GLN N 57 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR N 105 " --> pdb=" O THR N 121 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR N 121 " --> pdb=" O TYR N 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 152 through 155 removed outlier: 4.502A pdb=" N GLN N 152 " --> pdb=" O SER N 174 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER N 174 " --> pdb=" O GLN N 152 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.648A pdb=" N THR N 266 " --> pdb=" O GLU N 159 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL N 161 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR N 243 " --> pdb=" O THR N 263 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL N 242 " --> pdb=" O GLN N 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 167 through 168 removed outlier: 3.886A pdb=" N VAL N 167 " --> pdb=" O LEU N 232 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU N 232 " --> pdb=" O VAL N 167 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR N 229 " --> pdb=" O THR N 220 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR N 220 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 198 through 200 removed outlier: 3.665A pdb=" N TYR N 199 " --> pdb=" O LYS N 208 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS N 208 " --> pdb=" O TYR N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 240 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 125 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3651 1.34 - 1.45: 4702 1.45 - 1.57: 7515 1.57 - 1.69: 598 1.69 - 1.81: 58 Bond restraints: 16524 Sorted by residual: bond pdb=" C3' DA J 56 " pdb=" C2' DA J 56 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.26e+00 bond pdb=" C1' DT I 144 " pdb=" N1 DT I 144 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 3.92e+00 bond pdb=" C1' DC J 146 " pdb=" N1 DC J 146 " ideal model delta sigma weight residual 1.468 1.496 -0.028 1.40e-02 5.10e+03 3.90e+00 bond pdb=" C1' DC I 92 " pdb=" N1 DC I 92 " ideal model delta sigma weight residual 1.468 1.495 -0.027 1.40e-02 5.10e+03 3.85e+00 bond pdb=" C1' DC J 156 " pdb=" N1 DC J 156 " ideal model delta sigma weight residual 1.468 1.495 -0.027 1.40e-02 5.10e+03 3.83e+00 ... (remaining 16519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 22516 1.13 - 2.26: 922 2.26 - 3.39: 180 3.39 - 4.51: 0 4.51 - 5.64: 10 Bond angle restraints: 23628 Sorted by residual: angle pdb=" N3 DT J 108 " pdb=" C4 DT J 108 " pdb=" O4 DT J 108 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT J 27 " pdb=" C4 DT J 27 " pdb=" O4 DT J 27 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT I 10 " pdb=" C4 DT I 10 " pdb=" O4 DT I 10 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT I 142 " pdb=" C4 DT I 142 " pdb=" O4 DT I 142 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT I 153 " pdb=" C4 DT I 153 " pdb=" O4 DT I 153 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 23623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 7345 15.18 - 30.36: 783 30.36 - 45.54: 437 45.54 - 60.72: 564 60.72 - 75.90: 5 Dihedral angle restraints: 9134 sinusoidal: 5642 harmonic: 3492 Sorted by residual: dihedral pdb=" CB MET A 28 " pdb=" CG MET A 28 " pdb=" SD MET A 28 " pdb=" CE MET A 28 " ideal model delta sinusoidal sigma weight residual 60.00 112.20 -52.20 3 1.50e+01 4.44e-03 9.09e+00 dihedral pdb=" CB MET E 28 " pdb=" CG MET E 28 " pdb=" SD MET E 28 " pdb=" CE MET E 28 " ideal model delta sinusoidal sigma weight residual 60.00 111.23 -51.23 3 1.50e+01 4.44e-03 8.99e+00 dihedral pdb=" CA LEU A 82 " pdb=" CB LEU A 82 " pdb=" CG LEU A 82 " pdb=" CD1 LEU A 82 " ideal model delta sinusoidal sigma weight residual 180.00 129.77 50.23 3 1.50e+01 4.44e-03 8.88e+00 ... (remaining 9131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1175 0.025 - 0.050: 1028 0.050 - 0.075: 229 0.075 - 0.100: 198 0.100 - 0.126: 38 Chirality restraints: 2668 Sorted by residual: chirality pdb=" CA VAL N 77 " pdb=" N VAL N 77 " pdb=" C VAL N 77 " pdb=" CB VAL N 77 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA VAL M 77 " pdb=" N VAL M 77 " pdb=" C VAL M 77 " pdb=" CB VAL M 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.13e-01 chirality pdb=" CA ILE N 94 " pdb=" N ILE N 94 " pdb=" C ILE N 94 " pdb=" CB ILE N 94 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 2665 not shown) Planarity restraints: 1940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET G 121 " -0.010 5.00e-02 4.00e+02 1.55e-02 3.83e-01 pdb=" N PRO G 122 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO G 122 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO G 122 " -0.009 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 32 " 0.010 5.00e-02 4.00e+02 1.48e-02 3.53e-01 pdb=" N PRO H 33 " -0.026 5.00e-02 4.00e+02 pdb=" CA PRO H 33 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO H 33 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 77 " -0.010 5.00e-02 4.00e+02 1.46e-02 3.40e-01 pdb=" N PRO E 78 " 0.025 5.00e-02 4.00e+02 pdb=" CA PRO E 78 " -0.007 5.00e-02 4.00e+02 pdb=" CD PRO E 78 " -0.008 5.00e-02 4.00e+02 ... (remaining 1937 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4011 2.83 - 3.35: 11843 3.35 - 3.86: 24697 3.86 - 4.38: 29495 4.38 - 4.90: 44801 Nonbonded interactions: 114847 Sorted by model distance: nonbonded pdb=" OH TYR M 55 " pdb=" OG1 THR M 255 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR N 55 " pdb=" OG1 THR N 255 " model vdw 2.318 3.040 nonbonded pdb=" OG SER M 84 " pdb=" OG SER M 91 " model vdw 2.342 3.040 nonbonded pdb=" O GLU H 64 " pdb=" NH1 ARG H 68 " model vdw 2.371 3.120 nonbonded pdb=" OG1 THR D 81 " pdb=" OP1 DA J 114 " model vdw 2.373 3.040 ... (remaining 114842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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 individual isotropic 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.800 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3597 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 : 0.004 0.028 16528 Z= 0.391 Angle : 0.552 5.643 23636 Z= 0.499 Chirality : 0.040 0.126 2668 Planarity : 0.002 0.015 1940 Dihedral : 19.875 75.899 6886 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.32 % Favored : 90.92 % Rotamer: Outliers : 0.79 % Allowed : 5.21 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.15 (0.17), residues: 1178 helix: -4.99 (0.06), residues: 386 sheet: -2.63 (0.34), residues: 182 loop : -2.52 (0.20), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 73 TYR 0.002 0.000 TYR N 199 PHE 0.001 0.000 PHE G 105 TRP 0.001 0.000 TRP M 196 HIS 0.000 0.000 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.39 (16524) covalent geometry : angle 0.55196 / 0.50 (23628) SS BOND : bond 0.00025 / 0.01 ( 4) SS BOND : angle 0.03415 / 0.02 ( 8) hydrogen bonds : bond 0.37863 / 24.98 ( 285) hydrogen bonds : angle 10.12409 / 7.02 ( 756) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 48 TYR cc_start: 0.7407 (t80) cc_final: 0.7054 (t80) REVERT: M 108 LEU cc_start: 0.5780 (tp) cc_final: 0.5559 (tp) REVERT: N 170 PRO cc_start: 0.5552 (Cg_endo) cc_final: 0.5150 (Cg_exo) REVERT: N 184 GLN cc_start: 0.6125 (mm-40) cc_final: 0.5447 (tm-30) REVERT: N 258 TYR cc_start: 0.3418 (m-80) cc_final: 0.3064 (m-80) REVERT: N 263 THR cc_start: 0.6895 (m) cc_final: 0.5908 (m) outliers start: 8 outliers final: 4 residues processed: 185 average time/residue: 0.6127 time to fit residues: 124.2449 Evaluate side-chains 106 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain N residue 201 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 HIS A 66 ASN A 93 GLN E 36 HIS E 93 GLN B 96 GLN B 110 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN ** C 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 GLN ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN H 26 ASN M 25 GLN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 GLN M 154 GLN M 192 GLN N 25 GLN N 88 GLN N 110 HIS N 152 GLN N 154 GLN N 192 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.306335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.292471 restraints weight = 17716.169| |-----------------------------------------------------------------------------| r_work (start): 0.4896 rms_B_bonded: 0.41 r_work: 0.4701 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5737 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.130 16528 Z= 0.346 Angle : 0.974 16.277 23636 Z= 0.520 Chirality : 0.056 0.365 2668 Planarity : 0.008 0.094 1940 Dihedral : 24.774 71.890 4610 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.24 % Allowed : 9.92 % Favored : 86.84 % 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: -4.21 (0.19), residues: 1178 helix: -3.51 (0.14), residues: 482 sheet: -1.39 (0.38), residues: 190 loop : -2.43 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG H 79 TYR 0.035 0.004 TYR C 55 PHE 0.028 0.005 PHE M 117 TRP 0.022 0.003 TRP M 196 HIS 0.009 0.003 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.35 (16524) covalent geometry : angle 0.97368 / 0.52 (23628) SS BOND : bond 0.00556 / 0.28 ( 4) SS BOND : angle 1.27802 / 0.68 ( 8) hydrogen bonds : bond 0.11460 / 7.82 ( 285) hydrogen bonds : angle 5.59783 / 3.86 ( 756) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8024 (tp30) cc_final: 0.6960 (tp30) REVERT: E 28 MET cc_start: 0.8711 (mtt) cc_final: 0.8201 (mtt) REVERT: E 32 ILE cc_start: 0.7136 (OUTLIER) cc_final: 0.6695 (pt) REVERT: D 96 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7613 (mtt-85) REVERT: M 30 MET cc_start: -0.0406 (pmm) cc_final: -0.0794 (ppp) REVERT: M 247 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5828 (ppt170) REVERT: N 30 MET cc_start: 0.1511 (pmm) cc_final: -0.2402 (tmm) outliers start: 33 outliers final: 11 residues processed: 213 average time/residue: 0.7321 time to fit residues: 169.0962 Evaluate side-chains 154 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain M residue 51 TYR Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain N residue 19 MET Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 201 TYR Chi-restraints excluded: chain N residue 264 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 100 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 114 HIS G 109 ASN ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN M 88 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 GLN ** N 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.299743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.284443 restraints weight = 17524.608| |-----------------------------------------------------------------------------| r_work (start): 0.4842 rms_B_bonded: 0.50 r_work: 0.4656 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5866 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 16528 Z= 0.159 Angle : 0.571 8.404 23636 Z= 0.328 Chirality : 0.038 0.149 2668 Planarity : 0.004 0.047 1940 Dihedral : 24.803 71.392 4606 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.73 % Allowed : 14.15 % Favored : 82.12 % 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: -2.99 (0.21), residues: 1178 helix: -2.00 (0.19), residues: 520 sheet: -1.09 (0.39), residues: 192 loop : -2.15 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 191 TYR 0.021 0.002 TYR H 52 PHE 0.011 0.001 PHE E 23 TRP 0.012 0.001 TRP M 60 HIS 0.007 0.002 HIS G 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (16524) covalent geometry : angle 0.57116 / 0.33 (23628) SS BOND : bond 0.00170 / 0.08 ( 4) SS BOND : angle 0.80714 / 0.47 ( 8) hydrogen bonds : bond 0.08711 / 6.22 ( 285) hydrogen bonds : angle 4.17217 / 2.84 ( 756) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.363 Fit side-chains REVERT: A 89 GLU cc_start: 0.8010 (tp30) cc_final: 0.7035 (tp30) REVERT: E 28 MET cc_start: 0.8813 (mtt) cc_final: 0.8486 (mtt) REVERT: M 184 GLN cc_start: 0.6218 (mt0) cc_final: 0.5538 (tt0) REVERT: M 247 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5462 (ptt180) REVERT: N 30 MET cc_start: 0.1227 (pmm) cc_final: 0.0802 (pmm) outliers start: 38 outliers final: 13 residues processed: 166 average time/residue: 0.6898 time to fit residues: 125.1101 Evaluate side-chains 149 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 109 ASN Chi-restraints excluded: chain D residue 96 ARG Chi-restraints excluded: chain M residue 189 THR Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 201 TYR Chi-restraints excluded: chain N residue 267 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 chunk 60 optimal weight: 0.7980 chunk 3 optimal weight: 0.0970 chunk 144 optimal weight: 3.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 HIS F 48 GLN C 69 GLN G 114 HIS M 56 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 HIS M 188 GLN N 57 GLN N 188 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.279713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.257392 restraints weight = 16331.815| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 0.56 r_work: 0.4432 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 16528 Z= 0.220 Angle : 0.744 22.821 23636 Z= 0.405 Chirality : 0.046 0.409 2668 Planarity : 0.006 0.096 1940 Dihedral : 25.378 75.425 4604 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.81 % Allowed : 14.24 % Favored : 80.94 % Cbeta Deviations : 0.09 % 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: -2.17 (0.22), residues: 1178 helix: -1.15 (0.20), residues: 526 sheet: -0.61 (0.41), residues: 178 loop : -1.97 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 34 TYR 0.022 0.003 TYR N 203 PHE 0.032 0.003 PHE G 79 TRP 0.013 0.002 TRP M 196 HIS 0.015 0.003 HIS G 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.22 (16524) covalent geometry : angle 0.74331 / 0.41 (23628) SS BOND : bond 0.01567 / 0.59 ( 4) SS BOND : angle 1.33805 / 0.74 ( 8) hydrogen bonds : bond 0.08553 / 5.70 ( 285) hydrogen bonds : angle 4.17931 / 2.78 ( 756) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 43 VAL cc_start: 0.6502 (OUTLIER) cc_final: 0.6244 (m) REVERT: A 89 GLU cc_start: 0.8265 (tp30) cc_final: 0.7093 (tp30) REVERT: E 28 MET cc_start: 0.8950 (mtt) cc_final: 0.8732 (mtt) REVERT: B 36 GLU cc_start: 0.7335 (tt0) cc_final: 0.7107 (mt-10) REVERT: D 81 THR cc_start: 0.9096 (t) cc_final: 0.8802 (m) REVERT: M 106 TYR cc_start: 0.8627 (m-80) cc_final: 0.8414 (m-80) REVERT: M 247 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.5289 (ptt180) REVERT: N 30 MET cc_start: 0.0875 (pmm) cc_final: -0.1185 (ppp) REVERT: N 186 VAL cc_start: 0.6398 (t) cc_final: 0.6122 (t) outliers start: 49 outliers final: 11 residues processed: 208 average time/residue: 0.7939 time to fit residues: 178.4882 Evaluate side-chains 165 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 42 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 201 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 90 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 136 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 83 HIS F 48 GLN ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN M 56 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.272710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.248168 restraints weight = 16099.374| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 0.58 r_work: 0.4349 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.7901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16528 Z= 0.199 Angle : 0.667 17.499 23636 Z= 0.368 Chirality : 0.042 0.262 2668 Planarity : 0.005 0.087 1940 Dihedral : 25.775 77.836 4604 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.03 % Allowed : 16.01 % Favored : 79.96 % 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: -1.72 (0.23), residues: 1178 helix: -0.65 (0.21), residues: 538 sheet: -0.45 (0.40), residues: 188 loop : -1.93 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.001 ARG M 49 TYR 0.054 0.002 TYR M 51 PHE 0.016 0.002 PHE C 79 TRP 0.010 0.002 TRP N 259 HIS 0.008 0.002 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (16524) covalent geometry : angle 0.66733 / 0.37 (23628) SS BOND : bond 0.00445 / 0.17 ( 4) SS BOND : angle 0.61414 / 0.35 ( 8) hydrogen bonds : bond 0.06891 / 5.06 ( 285) hydrogen bonds : angle 3.81953 / 2.53 ( 756) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 174 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7981 (ptpp) REVERT: A 89 GLU cc_start: 0.8245 (tp30) cc_final: 0.7096 (tp30) REVERT: E 28 MET cc_start: 0.9003 (mtt) cc_final: 0.8758 (mtt) REVERT: E 89 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.5430 (tp30) REVERT: B 36 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: B 87 ARG cc_start: 0.7540 (mtt90) cc_final: 0.7235 (mmt90) REVERT: G 121 MET cc_start: 0.8642 (mmm) cc_final: 0.7785 (mtm) REVERT: D 81 THR cc_start: 0.9128 (t) cc_final: 0.8838 (m) REVERT: M 30 MET cc_start: 0.0631 (ppp) cc_final: 0.0419 (pmm) REVERT: M 106 TYR cc_start: 0.8765 (m-80) cc_final: 0.8554 (m-80) REVERT: M 188 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: M 247 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.5320 (ptt180) outliers start: 41 outliers final: 16 residues processed: 194 average time/residue: 0.7432 time to fit residues: 156.5032 Evaluate side-chains 175 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 188 GLN Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain N residue 42 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 130 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.0060 chunk 53 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 127 optimal weight: 0.0770 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 HIS C 109 ASN C 114 HIS M 56 GLN M 109 GLN M 154 GLN N 57 GLN N 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.274086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.247713 restraints weight = 16087.343| |-----------------------------------------------------------------------------| r_work (start): 0.4528 rms_B_bonded: 0.59 r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.8054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 16528 Z= 0.126 Angle : 0.550 17.997 23636 Z= 0.312 Chirality : 0.038 0.287 2668 Planarity : 0.004 0.038 1940 Dihedral : 25.706 78.547 4602 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.34 % Allowed : 18.07 % Favored : 78.59 % 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: -1.11 (0.23), residues: 1178 helix: 0.05 (0.22), residues: 542 sheet: -0.33 (0.41), residues: 188 loop : -1.83 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 49 TYR 0.017 0.001 TYR M 51 PHE 0.010 0.002 PHE N 117 TRP 0.010 0.001 TRP M 196 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.13 (16524) covalent geometry : angle 0.54948 / 0.31 (23628) SS BOND : bond 0.00176 / 0.07 ( 4) SS BOND : angle 0.85588 / 0.49 ( 8) hydrogen bonds : bond 0.06415 / 4.84 ( 285) hydrogen bonds : angle 3.49973 / 2.30 ( 756) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8073 (ptpp) cc_final: 0.7855 (ptpp) REVERT: A 89 GLU cc_start: 0.8007 (tp30) cc_final: 0.7061 (tp30) REVERT: E 28 MET cc_start: 0.9021 (mtt) cc_final: 0.8678 (mtt) REVERT: E 89 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.5229 (tp30) REVERT: B 36 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: B 87 ARG cc_start: 0.7290 (mtt90) cc_final: 0.6987 (mmt90) REVERT: G 126 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: D 81 THR cc_start: 0.9024 (t) cc_final: 0.8809 (m) REVERT: M 106 TYR cc_start: 0.8612 (m-80) cc_final: 0.8386 (m-80) REVERT: M 184 GLN cc_start: 0.6933 (mt0) cc_final: 0.6097 (tt0) REVERT: M 247 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5453 (ptt180) REVERT: N 19 MET cc_start: 0.3226 (OUTLIER) cc_final: 0.2822 (tpt) outliers start: 34 outliers final: 13 residues processed: 185 average time/residue: 0.7525 time to fit residues: 150.9646 Evaluate side-chains 170 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain M residue 109 GLN Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain N residue 19 MET Chi-restraints excluded: chain N residue 42 CYS Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 115 optimal weight: 0.0470 chunk 133 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 48 GLN D 26 ASN M 56 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN N 57 GLN N 188 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.272639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.246550 restraints weight = 15922.406| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 0.54 r_work: 0.4330 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.8250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16528 Z= 0.129 Angle : 0.547 16.677 23636 Z= 0.311 Chirality : 0.037 0.220 2668 Planarity : 0.004 0.034 1940 Dihedral : 25.738 77.925 4602 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.93 % Allowed : 17.39 % Favored : 78.68 % 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: -0.80 (0.24), residues: 1178 helix: 0.35 (0.22), residues: 542 sheet: -0.18 (0.41), residues: 188 loop : -1.74 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 251 TYR 0.019 0.001 TYR H 89 PHE 0.009 0.001 PHE C 79 TRP 0.008 0.001 TRP N 54 HIS 0.011 0.001 HIS M 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (16524) covalent geometry : angle 0.54654 / 0.31 (23628) SS BOND : bond 0.00203 / 0.08 ( 4) SS BOND : angle 0.70416 / 0.41 ( 8) hydrogen bonds : bond 0.06132 / 4.63 ( 285) hydrogen bonds : angle 3.47526 / 2.28 ( 756) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8288 (tp30) cc_final: 0.7118 (tp30) REVERT: A 112 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: E 28 MET cc_start: 0.9024 (mtt) cc_final: 0.8675 (mtt) REVERT: B 36 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7277 (mt-10) REVERT: B 87 ARG cc_start: 0.7539 (mtt90) cc_final: 0.7269 (mmt90) REVERT: G 126 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: D 81 THR cc_start: 0.9119 (t) cc_final: 0.8815 (m) REVERT: M 23 MET cc_start: 0.4217 (OUTLIER) cc_final: 0.3026 (ttm) REVERT: M 30 MET cc_start: 0.0387 (ppp) cc_final: -0.0065 (ppp) REVERT: M 184 GLN cc_start: 0.7107 (mt0) cc_final: 0.6080 (tt0) REVERT: M 218 THR cc_start: 0.7081 (m) cc_final: 0.6857 (p) REVERT: M 247 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.5454 (ptt180) REVERT: N 57 GLN cc_start: 0.8087 (tt0) cc_final: 0.7841 (tt0) outliers start: 40 outliers final: 18 residues processed: 180 average time/residue: 0.8021 time to fit residues: 156.0751 Evaluate side-chains 175 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain D residue 26 ASN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain M residue 23 MET Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 247 ARG Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 42 CYS Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 48 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 71 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 48 GLN ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 184 GLN N 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.262721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.237184 restraints weight = 15703.756| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 0.59 r_work: 0.4252 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.9121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 16528 Z= 0.196 Angle : 0.685 16.329 23636 Z= 0.379 Chirality : 0.045 0.425 2668 Planarity : 0.005 0.058 1940 Dihedral : 26.117 80.120 4602 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.42 % Allowed : 17.39 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % 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: -0.80 (0.24), residues: 1178 helix: 0.41 (0.22), residues: 536 sheet: -0.39 (0.39), residues: 204 loop : -1.71 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG N 251 TYR 0.024 0.002 TYR H 89 PHE 0.021 0.002 PHE C 79 TRP 0.014 0.002 TRP M 196 HIS 0.008 0.002 HIS N 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (16524) covalent geometry : angle 0.68482 / 0.38 (23628) SS BOND : bond 0.00355 / 0.17 ( 4) SS BOND : angle 1.17534 / 0.65 ( 8) hydrogen bonds : bond 0.06013 / 4.26 ( 285) hydrogen bonds : angle 3.87366 / 2.54 ( 756) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8233 (tp30) cc_final: 0.6895 (tp30) REVERT: A 112 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: E 75 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8739 (tpp-160) REVERT: B 87 ARG cc_start: 0.7627 (mtt90) cc_final: 0.7378 (mmt90) REVERT: F 87 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7791 (mmm-85) REVERT: G 78 ASP cc_start: 0.7657 (p0) cc_final: 0.7410 (m-30) REVERT: G 126 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8440 (mt0) REVERT: D 81 THR cc_start: 0.9173 (t) cc_final: 0.8811 (m) REVERT: M 30 MET cc_start: 0.0630 (OUTLIER) cc_final: 0.0126 (ppp) REVERT: N 23 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.6341 (mpp) REVERT: N 30 MET cc_start: 0.1125 (pmm) cc_final: -0.2568 (tmm) REVERT: N 57 GLN cc_start: 0.8091 (tt0) cc_final: 0.7835 (tt0) outliers start: 45 outliers final: 20 residues processed: 212 average time/residue: 0.7826 time to fit residues: 179.3771 Evaluate side-chains 193 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 112 GLU Chi-restraints excluded: chain E residue 75 ARG Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain G residue 46 THR Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain M residue 30 MET Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 23 MET Chi-restraints excluded: chain N residue 42 CYS Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 252 LEU Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 20.0000 chunk 139 optimal weight: 0.0270 chunk 89 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN F 48 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 56 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.264947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.241571 restraints weight = 15817.638| |-----------------------------------------------------------------------------| r_work (start): 0.4470 rms_B_bonded: 0.50 r_work: 0.4309 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work: 0.4258 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.9294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16528 Z= 0.141 Angle : 0.587 15.922 23636 Z= 0.331 Chirality : 0.039 0.253 2668 Planarity : 0.004 0.078 1940 Dihedral : 26.176 80.329 4602 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.75 % Allowed : 19.84 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1178 helix: 0.70 (0.22), residues: 536 sheet: -0.32 (0.38), residues: 212 loop : -1.69 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 34 TYR 0.022 0.002 TYR M 203 PHE 0.018 0.002 PHE M 213 TRP 0.010 0.001 TRP N 196 HIS 0.007 0.001 HIS G 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (16524) covalent geometry : angle 0.58685 / 0.33 (23628) SS BOND : bond 0.00435 / 0.17 ( 4) SS BOND : angle 0.77232 / 0.42 ( 8) hydrogen bonds : bond 0.05539 / 4.12 ( 285) hydrogen bonds : angle 3.80142 / 2.49 ( 756) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 VAL cc_start: 0.6567 (p) cc_final: 0.6339 (m) REVERT: A 89 GLU cc_start: 0.8224 (tp30) cc_final: 0.6910 (tp30) REVERT: B 87 ARG cc_start: 0.7606 (mtt90) cc_final: 0.7371 (mmt90) REVERT: F 53 THR cc_start: 0.8730 (m) cc_final: 0.8393 (m) REVERT: F 87 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7699 (mmt90) REVERT: G 126 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: D 81 THR cc_start: 0.9177 (t) cc_final: 0.8820 (m) REVERT: M 30 MET cc_start: 0.0548 (ppp) cc_final: 0.0065 (ppp) REVERT: M 184 GLN cc_start: 0.7069 (mt0) cc_final: 0.6058 (tt0) REVERT: N 30 MET cc_start: 0.1252 (pmm) cc_final: -0.2379 (tmm) REVERT: N 64 LYS cc_start: 0.7244 (pttt) cc_final: 0.6446 (pttp) outliers start: 28 outliers final: 13 residues processed: 183 average time/residue: 0.7747 time to fit residues: 153.4947 Evaluate side-chains 172 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 242 VAL Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 36 HIS ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 110 HIS G 69 GLN D 26 ASN ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 154 GLN N 57 GLN ** N 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.248499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.220414 restraints weight = 15221.280| |-----------------------------------------------------------------------------| r_work (start): 0.4279 rms_B_bonded: 0.52 r_work: 0.4081 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 1.0722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 16528 Z= 0.312 Angle : 0.921 16.583 23636 Z= 0.493 Chirality : 0.057 0.404 2668 Planarity : 0.008 0.091 1940 Dihedral : 27.085 83.666 4602 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 2.85 % Allowed : 19.25 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.23), residues: 1178 helix: 0.16 (0.22), residues: 540 sheet: -0.91 (0.34), residues: 212 loop : -1.79 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG N 251 TYR 0.032 0.004 TYR M 51 PHE 0.029 0.004 PHE C 79 TRP 0.024 0.003 TRP M 196 HIS 0.023 0.003 HIS G 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.31 (16524) covalent geometry : angle 0.92091 / 0.49 (23628) SS BOND : bond 0.01140 / 0.43 ( 4) SS BOND : angle 1.51158 / 0.88 ( 8) hydrogen bonds : bond 0.07014 / 4.63 ( 285) hydrogen bonds : angle 4.56212 / 2.96 ( 756) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8294 (tp30) cc_final: 0.6930 (tp30) REVERT: E 89 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6697 (tp30) REVERT: B 87 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7409 (mmt90) REVERT: G 126 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: D 81 THR cc_start: 0.9319 (t) cc_final: 0.8974 (m) REVERT: M 30 MET cc_start: 0.0534 (ppp) cc_final: 0.0063 (ppp) REVERT: M 39 THR cc_start: 0.7450 (m) cc_final: 0.7227 (t) REVERT: N 19 MET cc_start: 0.3767 (OUTLIER) cc_final: 0.3539 (tpt) REVERT: N 30 MET cc_start: 0.1751 (pmm) cc_final: -0.2165 (tmm) REVERT: N 53 SER cc_start: 0.7916 (OUTLIER) cc_final: 0.7117 (t) REVERT: N 55 TYR cc_start: 0.6539 (m-80) cc_final: 0.6164 (m-80) REVERT: N 64 LYS cc_start: 0.7537 (pttt) cc_final: 0.7154 (ptmt) outliers start: 29 outliers final: 12 residues processed: 224 average time/residue: 0.7812 time to fit residues: 189.2327 Evaluate side-chains 199 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain G residue 126 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain M residue 183 ILE Chi-restraints excluded: chain M residue 267 VAL Chi-restraints excluded: chain N residue 19 MET Chi-restraints excluded: chain N residue 42 CYS Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 183 ILE Chi-restraints excluded: chain N residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 40.0000 chunk 80 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 110 HIS C 126 GLN ** D 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN M 56 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 GLN N 57 GLN N 110 HIS N 188 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.251311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.224701 restraints weight = 15181.103| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 0.54 r_work: 0.4153 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 1.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 16528 Z= 0.170 Angle : 0.649 14.843 23636 Z= 0.367 Chirality : 0.043 0.310 2668 Planarity : 0.005 0.055 1940 Dihedral : 26.996 82.056 4602 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.36 % Allowed : 21.81 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.23), residues: 1178 helix: 0.35 (0.22), residues: 552 sheet: -0.88 (0.35), residues: 212 loop : -1.60 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 93 TYR 0.026 0.002 TYR M 51 PHE 0.016 0.002 PHE C 79 TRP 0.014 0.002 TRP N 196 HIS 0.014 0.002 HIS G 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (16524) covalent geometry : angle 0.64914 / 0.37 (23628) SS BOND : bond 0.00375 / 0.15 ( 4) SS BOND : angle 1.07640 / 0.63 ( 8) hydrogen bonds : bond 0.05450 / 3.76 ( 285) hydrogen bonds : angle 4.23953 / 2.76 ( 756) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4444.10 seconds wall clock time: 76 minutes 43.51 seconds (4603.51 seconds total)