Starting phenix.real_space_refine on Mon Sep 23 21:13:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/09_2024/6w7m_21571.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/09_2024/6w7m_21571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/09_2024/6w7m_21571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/09_2024/6w7m_21571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/09_2024/6w7m_21571.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/09_2024/6w7m_21571.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.035 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 1512 5.49 5 S 65 5.16 5 C 25893 2.51 5 N 9458 2.21 5 O 13766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 50694 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 32448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1512, 32448 Classifications: {'RNA': 1512} Modifications used: {'rna2p_pur': 114, 'rna2p_pyr': 84, 'rna3p_pur': 749, 'rna3p_pyr': 565} Link IDs: {'rna2p': 197, 'rna3p': 1314} Chain breaks: 2 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "G" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1163 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "L" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "O" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Time building chain proxies: 20.35, per 1000 atoms: 0.40 Number of scatterers: 50694 At special positions: 0 Unit cell: (204.943, 219.965, 169.534, 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 65 16.00 P 1512 15.00 O 13766 8.00 N 9458 7.00 C 25893 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.66 Conformation dependent library (CDL) restraints added in 2.2 seconds 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4294 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 23 sheets defined 41.6% alpha, 15.2% beta 482 base pairs and 740 stacking pairs defined. Time for finding SS restraints: 16.77 Creating SS restraints... Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.659A pdb=" N MET B 26 " --> pdb=" O ASN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 62 removed outlier: 4.001A pdb=" N MET B 48 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 121 removed outlier: 4.474A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 removed outlier: 3.901A pdb=" N GLU B 139 " --> pdb=" O MET B 135 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 Processing helix chain 'B' and resid 205 through 222 removed outlier: 3.590A pdb=" N VAL B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.734A pdb=" N ILE C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 10' Processing helix chain 'C' and resid 27 through 46 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 80 through 95 removed outlier: 4.595A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 110 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.569A pdb=" N VAL C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 4.438A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N MET C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 179 Processing helix chain 'D' and resid 8 through 16 removed outlier: 4.077A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.551A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 27 through 32' Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 110 through 119 removed outlier: 3.598A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 150 removed outlier: 3.589A pdb=" N LYS D 150 " --> pdb=" O GLU D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 152 through 165 removed outlier: 4.116A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 4.213A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 110 through 118 Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 158 removed outlier: 3.674A pdb=" N GLY E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 12 through 15 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.843A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 104 Processing helix chain 'G' and resid 19 through 30 Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.841A pdb=" N SER G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 66 Processing helix chain 'G' and resid 91 through 105 removed outlier: 3.732A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 128 removed outlier: 3.579A pdb=" N SER G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 removed outlier: 3.593A pdb=" N ALA G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'H' and resid 5 through 19 removed outlier: 3.572A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.667A pdb=" N LEU H 92 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 removed outlier: 4.067A pdb=" N ALA H 97 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'I' and resid 33 through 38 removed outlier: 3.842A pdb=" N TYR I 37 " --> pdb=" O SER I 33 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 33 through 38' Processing helix chain 'I' and resid 43 through 47 removed outlier: 3.976A pdb=" N VAL I 46 " --> pdb=" O ALA I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 70 through 90 removed outlier: 3.537A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU I 88 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 100 removed outlier: 4.216A pdb=" N ALA I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 28 removed outlier: 4.529A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 58 removed outlier: 3.707A pdb=" N ARG K 56 " --> pdb=" O ARG K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 75 removed outlier: 4.214A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 103 removed outlier: 3.940A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 9 removed outlier: 3.929A pdb=" N ARG L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.624A pdb=" N GLY L 118 " --> pdb=" O SER L 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 19 Processing helix chain 'M' and resid 27 through 35 removed outlier: 4.110A pdb=" N LEU M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA M 34 " --> pdb=" O LYS M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 Processing helix chain 'M' and resid 54 through 61 removed outlier: 3.560A pdb=" N ASP M 57 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU M 58 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL M 59 " --> pdb=" O ARG M 56 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA M 60 " --> pdb=" O ASP M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 81 Processing helix chain 'M' and resid 84 through 92 Processing helix chain 'N' and resid 2 through 19 removed outlier: 3.592A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 9 " --> pdb=" O MET N 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA N 14 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 31 removed outlier: 4.259A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 48 removed outlier: 3.677A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 89 removed outlier: 3.608A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 39 removed outlier: 3.518A pdb=" N GLN O 28 " --> pdb=" O SER O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.538A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 removed outlier: 3.655A pdb=" N GLY O 86 " --> pdb=" O ILE O 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 82 removed outlier: 4.703A pdb=" N ALA P 82 " --> pdb=" O VAL P 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.622A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 31 removed outlier: 3.553A pdb=" N LEU R 29 " --> pdb=" O ASP R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 removed outlier: 4.261A pdb=" N THR R 45 " --> pdb=" O PRO R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'S' and resid 11 through 23 removed outlier: 4.658A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 44 removed outlier: 3.511A pdb=" N ILE S 44 " --> pdb=" O PRO S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 74 Processing helix chain 'T' and resid 4 through 42 removed outlier: 3.835A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 84 removed outlier: 3.800A pdb=" N ALA T 72 " --> pdb=" O HIS T 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.552A pdb=" N ILE B 39 " --> pdb=" O PHE B 31 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA B 33 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.092A pdb=" N PHE B 89 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 160 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE B 185 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 55 removed outlier: 6.537A pdb=" N HIS C 68 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE C 54 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 66 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 103 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 69 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.538A pdb=" N LYS C 149 " --> pdb=" O TRP C 200 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 130 removed outlier: 4.218A pdb=" N ILE D 123 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 12 through 24 removed outlier: 3.658A pdb=" N VAL E 38 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL E 18 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR E 34 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG E 20 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N SER E 32 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SER E 22 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE E 30 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL E 46 " --> pdb=" O ILE E 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 85 through 88 removed outlier: 6.826A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 35 through 46 removed outlier: 6.295A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP F 41 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N TYR F 59 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY F 43 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA F 57 " --> pdb=" O GLY F 43 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 72 through 74 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'H' and resid 24 through 28 removed outlier: 6.051A pdb=" N GLU H 58 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL H 51 " --> pdb=" O GLU H 58 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU H 60 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE H 49 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR H 62 " --> pdb=" O GLU H 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 65 through 66 Processing sheet with id=AB4, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.683A pdb=" N GLY H 123 " --> pdb=" O LYS H 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 74 through 77 removed outlier: 7.175A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR H 128 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE H 101 " --> pdb=" O TYR H 128 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.838A pdb=" N GLY I 7 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL I 18 " --> pdb=" O GLY I 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 45 through 48 Processing sheet with id=AB8, first strand: chain 'J' and resid 45 through 48 removed outlier: 3.761A pdb=" N GLU J 66 " --> pdb=" O LYS N 96 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS N 96 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 41 through 43 removed outlier: 6.387A pdb=" N ILE K 34 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ALA K 21 " --> pdb=" O MET K 85 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU K 82 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN K 109 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR K 111 " --> pdb=" O VAL K 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 62 through 66 removed outlier: 7.225A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 72 through 73 Processing sheet with id=AC3, first strand: chain 'P' and resid 50 through 51 removed outlier: 3.758A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE P 38 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 8 through 14 removed outlier: 7.997A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG Q 11 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU Q 75 " --> pdb=" O HIS Q 47 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 30 through 32 removed outlier: 4.036A pdb=" N LEU S 30 " --> pdb=" O THR S 47 " (cutoff:3.500A) 754 hydrogen bonds defined for protein. 2121 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1216 hydrogen bonds 1988 hydrogen bond angles 0 basepair planarities 482 basepair parallelities 740 stacking parallelities Total time for adding SS restraints: 40.27 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4412 1.28 - 1.41: 18053 1.41 - 1.55: 29200 1.55 - 1.68: 3061 1.68 - 1.81: 116 Bond restraints: 54842 Sorted by residual: bond pdb=" C2 C A1158 " pdb=" O2 C A1158 " ideal model delta sigma weight residual 1.240 1.146 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" N THR B 129 " pdb=" CA THR B 129 " ideal model delta sigma weight residual 1.457 1.502 -0.046 1.32e-02 5.74e+03 1.19e+01 bond pdb=" C1' C A1158 " pdb=" N1 C A1158 " ideal model delta sigma weight residual 1.480 1.521 -0.041 1.50e-02 4.44e+03 7.35e+00 bond pdb=" C LEU B 128 " pdb=" N THR B 129 " ideal model delta sigma weight residual 1.332 1.369 -0.037 1.37e-02 5.33e+03 7.24e+00 bond pdb=" C5' C A1158 " pdb=" C4' C A1158 " ideal model delta sigma weight residual 1.508 1.543 -0.035 1.50e-02 4.44e+03 5.33e+00 ... (remaining 54837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 80700 2.32 - 4.63: 735 4.63 - 6.95: 74 6.95 - 9.26: 11 9.26 - 11.58: 4 Bond angle restraints: 81524 Sorted by residual: angle pdb=" C2' A A1157 " pdb=" C1' A A1157 " pdb=" N9 A A1157 " ideal model delta sigma weight residual 114.00 122.34 -8.34 1.50e+00 4.44e-01 3.09e+01 angle pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " ideal model delta sigma weight residual 108.50 116.12 -7.62 1.50e+00 4.44e-01 2.58e+01 angle pdb=" N THR B 129 " pdb=" CA THR B 129 " pdb=" C THR B 129 " ideal model delta sigma weight residual 110.35 116.98 -6.63 1.40e+00 5.10e-01 2.25e+01 angle pdb=" N VAL M 59 " pdb=" CA VAL M 59 " pdb=" C VAL M 59 " ideal model delta sigma weight residual 113.07 107.12 5.95 1.36e+00 5.41e-01 1.91e+01 angle pdb=" C LYS B 131 " pdb=" N GLU B 132 " pdb=" CA GLU B 132 " ideal model delta sigma weight residual 121.94 113.75 8.19 2.00e+00 2.50e-01 1.68e+01 ... (remaining 81519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 30753 35.74 - 71.49: 3891 71.49 - 107.23: 440 107.23 - 142.98: 13 142.98 - 178.72: 14 Dihedral angle restraints: 35111 sinusoidal: 28468 harmonic: 6643 Sorted by residual: dihedral pdb=" C4' A A1431 " pdb=" C3' A A1431 " pdb=" C2' A A1431 " pdb=" C1' A A1431 " ideal model delta sinusoidal sigma weight residual -35.00 30.58 -65.58 1 8.00e+00 1.56e-02 8.80e+01 dihedral pdb=" O4' C A1158 " pdb=" C1' C A1158 " pdb=" N1 C A1158 " pdb=" C2 C A1158 " ideal model delta sinusoidal sigma weight residual 200.00 34.57 165.43 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' U A 467 " pdb=" C1' U A 467 " pdb=" N1 U A 467 " pdb=" C2 U A 467 " ideal model delta sinusoidal sigma weight residual 200.00 35.81 164.19 1 1.50e+01 4.44e-03 8.37e+01 ... (remaining 35108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 9888 0.076 - 0.152: 406 0.152 - 0.227: 42 0.227 - 0.303: 5 0.303 - 0.379: 1 Chirality restraints: 10342 Sorted by residual: chirality pdb=" C1' C A1158 " pdb=" O4' C A1158 " pdb=" C2' C A1158 " pdb=" N1 C A1158 " both_signs ideal model delta sigma weight residual False 2.47 2.09 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C1' A A1157 " pdb=" O4' A A1157 " pdb=" C2' A A1157 " pdb=" N9 A A1157 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1' A A 179 " pdb=" O4' A A 179 " pdb=" C2' A A 179 " pdb=" N9 A A 179 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 10339 not shown) Planarity restraints: 4723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 518 " 0.000 2.00e-02 2.50e+03 3.71e-02 3.10e+01 pdb=" N1 C A 518 " -0.008 2.00e-02 2.50e+03 pdb=" C2 C A 518 " 0.096 2.00e-02 2.50e+03 pdb=" O2 C A 518 " -0.050 2.00e-02 2.50e+03 pdb=" N3 C A 518 " -0.021 2.00e-02 2.50e+03 pdb=" C4 C A 518 " -0.000 2.00e-02 2.50e+03 pdb=" N4 C A 518 " 0.002 2.00e-02 2.50e+03 pdb=" C5 C A 518 " -0.010 2.00e-02 2.50e+03 pdb=" C6 C A 518 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1157 " -0.057 2.00e-02 2.50e+03 2.90e-02 2.31e+01 pdb=" N9 A A1157 " 0.074 2.00e-02 2.50e+03 pdb=" C8 A A1157 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A1157 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A1157 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A A1157 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A A1157 " -0.019 2.00e-02 2.50e+03 pdb=" N1 A A1157 " 0.007 2.00e-02 2.50e+03 pdb=" C2 A A1157 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A1157 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A A1157 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 530 " 0.010 2.00e-02 2.50e+03 2.64e-02 2.09e+01 pdb=" N9 G A 530 " 0.002 2.00e-02 2.50e+03 pdb=" C8 G A 530 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 530 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G A 530 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G A 530 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G A 530 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G A 530 " 0.031 2.00e-02 2.50e+03 pdb=" C2 G A 530 " -0.077 2.00e-02 2.50e+03 pdb=" N2 G A 530 " 0.038 2.00e-02 2.50e+03 pdb=" N3 G A 530 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A 530 " -0.002 2.00e-02 2.50e+03 ... (remaining 4720 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 1069 2.61 - 3.18: 40754 3.18 - 3.75: 98006 3.75 - 4.33: 126880 4.33 - 4.90: 174974 Nonbonded interactions: 441683 Sorted by model distance: nonbonded pdb=" N6 A A1157 " pdb=" N2 G A1178 " model vdw 2.031 2.560 nonbonded pdb=" O2' A A 977 " pdb=" O4 U A 982 " model vdw 2.039 3.040 nonbonded pdb=" O6 G A1242 " pdb=" O4 U A1295 " model vdw 2.054 2.432 nonbonded pdb=" O2' G A 107 " pdb=" O2' G A 378 " model vdw 2.057 3.040 nonbonded pdb=" O2' A A1374 " pdb=" O ASN G 27 " model vdw 2.107 3.040 ... (remaining 441678 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.420 Check model and map are aligned: 0.290 Set scattering table: 0.340 Process input model: 111.710 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 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 : 0.002 0.094 54842 Z= 0.140 Angle : 0.584 11.578 81524 Z= 0.321 Chirality : 0.033 0.379 10342 Planarity : 0.004 0.049 4723 Dihedral : 23.743 178.724 30817 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.42 % Favored : 92.28 % Rotamer: Outliers : 0.10 % Allowed : 5.89 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.15), residues: 2279 helix: -1.91 (0.15), residues: 823 sheet: -2.17 (0.26), residues: 344 loop : -2.95 (0.16), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 200 HIS 0.006 0.001 HIS T 75 PHE 0.019 0.001 PHE J 49 TYR 0.008 0.001 TYR R 64 ARG 0.008 0.000 ARG K 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 527 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.3636 (tp30) cc_final: 0.2803 (mt-10) REVERT: B 99 MET cc_start: 0.4089 (ptm) cc_final: 0.3222 (ppp) REVERT: C 22 PHE cc_start: 0.2430 (t80) cc_final: 0.1991 (t80) REVERT: C 33 ASP cc_start: 0.3342 (t0) cc_final: 0.3014 (t0) REVERT: C 113 LYS cc_start: 0.6577 (mtpt) cc_final: 0.6210 (mtmt) REVERT: D 76 TYR cc_start: 0.7729 (t80) cc_final: 0.7455 (t80) REVERT: D 116 GLN cc_start: 0.7336 (tt0) cc_final: 0.7071 (tt0) REVERT: G 143 MET cc_start: -0.1615 (ptt) cc_final: -0.1912 (ptt) REVERT: I 56 MET cc_start: 0.0697 (ppp) cc_final: 0.0405 (ptt) REVERT: I 87 MET cc_start: 0.3431 (ptp) cc_final: 0.3182 (ptp) REVERT: O 71 LYS cc_start: 0.8316 (tttt) cc_final: 0.7911 (tttt) REVERT: P 80 LYS cc_start: 0.3623 (tttt) cc_final: 0.3221 (tttt) REVERT: R 44 ILE cc_start: 0.8298 (mp) cc_final: 0.7918 (mt) REVERT: S 19 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6168 (pt0) REVERT: S 65 MET cc_start: -0.2086 (mmt) cc_final: -0.3166 (ptt) REVERT: T 16 LYS cc_start: 0.8099 (mttm) cc_final: 0.7828 (mttt) outliers start: 2 outliers final: 0 residues processed: 528 average time/residue: 0.6924 time to fit residues: 562.5492 Evaluate side-chains 349 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 0.2980 chunk 96 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 217 optimal weight: 0.7980 chunk 337 optimal weight: 8.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS B 18 GLN B 102 ASN B 119 GLN B 145 ASN C 139 ASN C 175 HIS C 189 HIS D 41 HIS D 74 ASN D 126 ASN D 131 ASN ** D 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN E 70 ASN F 3 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN K 118 HIS L 6 GLN L 77 HIS ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN N 59 GLN O 28 GLN O 35 GLN O 46 HIS P 9 HIS P 63 GLN ** R 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 HIS S 56 HIS T 61 GLN T 68 HIS T 75 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 54842 Z= 0.307 Angle : 0.833 13.166 81524 Z= 0.416 Chirality : 0.043 0.505 10342 Planarity : 0.007 0.077 4723 Dihedral : 24.570 179.743 26209 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.71 % Favored : 89.16 % Rotamer: Outliers : 3.34 % Allowed : 17.62 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.16), residues: 2279 helix: -1.35 (0.16), residues: 828 sheet: -2.20 (0.25), residues: 347 loop : -2.83 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP Q 73 HIS 0.011 0.002 HIS T 20 PHE 0.020 0.003 PHE F 8 TYR 0.024 0.003 TYR N 19 ARG 0.017 0.001 ARG T 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 380 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 PHE cc_start: 0.6503 (m-10) cc_final: 0.5672 (t80) REVERT: B 51 GLU cc_start: 0.3839 (tp30) cc_final: 0.2858 (mt-10) REVERT: B 90 PHE cc_start: 0.3941 (p90) cc_final: 0.3175 (p90) REVERT: B 99 MET cc_start: 0.4190 (ptm) cc_final: 0.3320 (ppp) REVERT: C 113 LYS cc_start: 0.6756 (mtpt) cc_final: 0.6433 (mtmt) REVERT: C 146 LYS cc_start: 0.7385 (ptpp) cc_final: 0.7022 (ptpp) REVERT: C 178 ARG cc_start: 0.6651 (ttp-110) cc_final: 0.6327 (ttp-170) REVERT: D 4 TYR cc_start: 0.6638 (t80) cc_final: 0.6363 (t80) REVERT: D 116 GLN cc_start: 0.7167 (tt0) cc_final: 0.6846 (tt0) REVERT: F 88 MET cc_start: 0.5832 (ttt) cc_final: 0.5386 (ttt) REVERT: G 143 MET cc_start: -0.1626 (ptt) cc_final: -0.1836 (ptt) REVERT: J 80 THR cc_start: 0.4538 (OUTLIER) cc_final: 0.4189 (m) REVERT: M 104 ASN cc_start: 0.3913 (OUTLIER) cc_final: 0.3473 (t160) REVERT: N 74 ARG cc_start: 0.6865 (mtt180) cc_final: 0.6523 (mtt180) REVERT: S 19 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6157 (pt0) REVERT: S 65 MET cc_start: -0.0923 (mmt) cc_final: -0.3595 (ptt) REVERT: T 36 TYR cc_start: 0.5943 (m-80) cc_final: 0.5460 (m-80) REVERT: T 51 PHE cc_start: 0.8399 (t80) cc_final: 0.8171 (t80) outliers start: 64 outliers final: 39 residues processed: 412 average time/residue: 0.6055 time to fit residues: 391.5100 Evaluate side-chains 368 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 327 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 77 HIS Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 104 ASN Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 338 optimal weight: 0.3980 chunk 365 optimal weight: 0.9990 chunk 301 optimal weight: 0.0670 chunk 335 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 54842 Z= 0.191 Angle : 0.680 12.682 81524 Z= 0.343 Chirality : 0.038 0.483 10342 Planarity : 0.005 0.061 4723 Dihedral : 24.400 179.542 26209 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.35 % Favored : 90.48 % Rotamer: Outliers : 3.34 % Allowed : 21.22 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.16), residues: 2279 helix: -0.76 (0.17), residues: 836 sheet: -2.02 (0.26), residues: 343 loop : -2.58 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP Q 73 HIS 0.023 0.002 HIS T 75 PHE 0.015 0.002 PHE O 43 TYR 0.017 0.002 TYR R 32 ARG 0.010 0.001 ARG K 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 349 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 PHE cc_start: 0.6497 (m-80) cc_final: 0.5849 (t80) REVERT: B 51 GLU cc_start: 0.3797 (tp30) cc_final: 0.3110 (mt-10) REVERT: B 90 PHE cc_start: 0.3888 (p90) cc_final: 0.3241 (p90) REVERT: B 99 MET cc_start: 0.4111 (ptm) cc_final: 0.3375 (ppp) REVERT: C 64 ARG cc_start: 0.6785 (tmm-80) cc_final: 0.6309 (mmm160) REVERT: C 113 LYS cc_start: 0.6701 (mtpt) cc_final: 0.6305 (mtmt) REVERT: E 54 ARG cc_start: 0.7398 (tpt170) cc_final: 0.6731 (mmm160) REVERT: F 102 MET cc_start: 0.6769 (mpp) cc_final: 0.6457 (mpp) REVERT: G 143 MET cc_start: -0.0808 (ptt) cc_final: -0.1013 (ptt) REVERT: H 101 ILE cc_start: 0.5227 (OUTLIER) cc_final: 0.5021 (pt) REVERT: J 80 THR cc_start: 0.4352 (OUTLIER) cc_final: 0.3976 (m) REVERT: K 100 LEU cc_start: 0.6044 (mt) cc_final: 0.5521 (tp) REVERT: L 20 ASN cc_start: 0.8060 (p0) cc_final: 0.7724 (m-40) REVERT: M 80 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.4809 (tmm) REVERT: N 74 ARG cc_start: 0.6840 (mtt180) cc_final: 0.6560 (mtt180) REVERT: Q 11 ARG cc_start: 0.7520 (mtp-110) cc_final: 0.7305 (mtp85) REVERT: Q 49 GLU cc_start: 0.7602 (mp0) cc_final: 0.7050 (mp0) REVERT: S 19 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6310 (pt0) REVERT: S 65 MET cc_start: -0.0688 (mmt) cc_final: -0.3787 (ptt) REVERT: T 36 TYR cc_start: 0.5818 (m-80) cc_final: 0.5387 (m-80) REVERT: T 51 PHE cc_start: 0.8350 (t80) cc_final: 0.8048 (t80) outliers start: 64 outliers final: 40 residues processed: 386 average time/residue: 0.5790 time to fit residues: 358.8765 Evaluate side-chains 353 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 310 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 HIS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 176 ASN ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN D 131 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN L 77 HIS ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 HIS P 29 ASN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5939 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 54842 Z= 0.240 Angle : 0.757 13.064 81524 Z= 0.380 Chirality : 0.041 0.496 10342 Planarity : 0.006 0.063 4723 Dihedral : 24.512 179.784 26209 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.93 % Favored : 88.85 % Rotamer: Outliers : 5.06 % Allowed : 22.37 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.16), residues: 2279 helix: -0.82 (0.17), residues: 846 sheet: -2.04 (0.26), residues: 336 loop : -2.55 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP Q 73 HIS 0.015 0.002 HIS T 75 PHE 0.014 0.002 PHE P 39 TYR 0.021 0.002 TYR N 19 ARG 0.008 0.001 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 340 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 29 PHE cc_start: 0.6605 (m-80) cc_final: 0.5726 (t80) REVERT: B 51 GLU cc_start: 0.3950 (tp30) cc_final: 0.3285 (mt-10) REVERT: B 90 PHE cc_start: 0.3985 (p90) cc_final: 0.3313 (p90) REVERT: C 42 LEU cc_start: 0.6020 (pp) cc_final: 0.5378 (mt) REVERT: C 113 LYS cc_start: 0.6709 (mtpt) cc_final: 0.6494 (mtmt) REVERT: C 146 LYS cc_start: 0.7509 (ptpp) cc_final: 0.7121 (ptpp) REVERT: C 178 ARG cc_start: 0.6852 (ttp-110) cc_final: 0.6456 (ttp-170) REVERT: D 76 TYR cc_start: 0.8067 (t80) cc_final: 0.7731 (t80) REVERT: D 124 MET cc_start: 0.4399 (mtt) cc_final: 0.3623 (mtt) REVERT: E 54 ARG cc_start: 0.7473 (tpt170) cc_final: 0.6707 (mmm-85) REVERT: E 64 MET cc_start: 0.7937 (tpp) cc_final: 0.7595 (tpp) REVERT: G 143 MET cc_start: -0.1004 (ptt) cc_final: -0.1216 (ptt) REVERT: J 56 HIS cc_start: 0.4842 (OUTLIER) cc_final: 0.3623 (t70) REVERT: J 80 THR cc_start: 0.4630 (OUTLIER) cc_final: 0.4285 (m) REVERT: K 100 LEU cc_start: 0.6330 (mt) cc_final: 0.5800 (tp) REVERT: M 80 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5165 (tmm) REVERT: M 104 ASN cc_start: 0.4528 (m-40) cc_final: 0.3878 (m-40) REVERT: N 26 LEU cc_start: 0.5543 (OUTLIER) cc_final: 0.5109 (tp) REVERT: N 70 HIS cc_start: 0.6897 (m-70) cc_final: 0.6643 (m-70) REVERT: N 74 ARG cc_start: 0.6912 (mtt180) cc_final: 0.6656 (mtt180) REVERT: S 19 GLU cc_start: 0.7367 (tm-30) cc_final: 0.6019 (pt0) REVERT: T 9 LYS cc_start: 0.5973 (OUTLIER) cc_final: 0.5630 (pttp) REVERT: T 36 TYR cc_start: 0.6216 (m-80) cc_final: 0.5718 (m-80) REVERT: T 51 PHE cc_start: 0.8343 (t80) cc_final: 0.8051 (t80) outliers start: 97 outliers final: 68 residues processed: 408 average time/residue: 0.6687 time to fit residues: 442.2560 Evaluate side-chains 390 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 317 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 HIS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 80 MET Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 75 LYS Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 HIS Chi-restraints excluded: chain O residue 83 GLU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 51 HIS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 35 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 0.0470 chunk 148 optimal weight: 10.0000 chunk 306 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 322 optimal weight: 0.0000 chunk 90 optimal weight: 8.9990 overall best weight: 0.5282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 116 GLN E 70 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS L 96 HIS M 13 HIS T 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 54842 Z= 0.149 Angle : 0.630 12.676 81524 Z= 0.317 Chirality : 0.035 0.496 10342 Planarity : 0.005 0.085 4723 Dihedral : 24.259 179.719 26209 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.85 % Favored : 91.97 % Rotamer: Outliers : 3.23 % Allowed : 25.34 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.17), residues: 2279 helix: -0.27 (0.18), residues: 845 sheet: -1.75 (0.27), residues: 340 loop : -2.23 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 73 HIS 0.023 0.001 HIS L 77 PHE 0.010 0.001 PHE B 49 TYR 0.016 0.001 TYR R 32 ARG 0.011 0.001 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 350 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.3971 (tp30) cc_final: 0.3375 (mt-10) REVERT: B 90 PHE cc_start: 0.3645 (p90) cc_final: 0.3053 (p90) REVERT: C 42 LEU cc_start: 0.5983 (pp) cc_final: 0.5354 (tt) REVERT: C 113 LYS cc_start: 0.6735 (mtpt) cc_final: 0.6305 (mtmt) REVERT: C 146 LYS cc_start: 0.7270 (ptpp) cc_final: 0.6885 (ptpp) REVERT: C 178 ARG cc_start: 0.6761 (ttp-110) cc_final: 0.6386 (ttp-170) REVERT: D 8 LYS cc_start: 0.7980 (mttp) cc_final: 0.7487 (mtpt) REVERT: D 76 TYR cc_start: 0.7918 (t80) cc_final: 0.7533 (t80) REVERT: D 124 MET cc_start: 0.4217 (mtt) cc_final: 0.3717 (mtt) REVERT: D 201 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.6957 (t) REVERT: E 54 ARG cc_start: 0.7223 (tpt170) cc_final: 0.6706 (mmm-85) REVERT: E 64 MET cc_start: 0.7620 (tpp) cc_final: 0.7403 (tpp) REVERT: E 82 GLN cc_start: 0.4896 (OUTLIER) cc_final: 0.4269 (mp10) REVERT: F 1 MET cc_start: 0.4180 (mpp) cc_final: 0.3717 (ptp) REVERT: G 143 MET cc_start: -0.0912 (ptt) cc_final: -0.1139 (ptt) REVERT: H 10 MET cc_start: 0.5415 (ttp) cc_final: 0.4629 (tpp) REVERT: K 100 LEU cc_start: 0.5586 (mt) cc_final: 0.5316 (tp) REVERT: L 62 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5501 (mm-30) REVERT: N 70 HIS cc_start: 0.6825 (m-70) cc_final: 0.6550 (m-70) REVERT: O 56 LEU cc_start: 0.7770 (tt) cc_final: 0.7394 (tp) REVERT: S 19 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6162 (pt0) REVERT: T 36 TYR cc_start: 0.6142 (m-80) cc_final: 0.5636 (m-80) outliers start: 62 outliers final: 40 residues processed: 393 average time/residue: 0.5838 time to fit residues: 361.6455 Evaluate side-chains 354 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 312 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 HIS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 10.0000 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 0.0170 chunk 88 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 overall best weight: 5.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 116 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS K 29 ASN K 109 ASN L 77 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 54842 Z= 0.352 Angle : 0.933 14.510 81524 Z= 0.466 Chirality : 0.048 0.469 10342 Planarity : 0.008 0.106 4723 Dihedral : 24.843 179.001 26209 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.46 % Favored : 87.36 % Rotamer: Outliers : 5.58 % Allowed : 25.50 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.16), residues: 2279 helix: -1.04 (0.16), residues: 854 sheet: -1.97 (0.26), residues: 336 loop : -2.65 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP Q 73 HIS 0.013 0.002 HIS T 20 PHE 0.024 0.003 PHE P 39 TYR 0.029 0.003 TYR R 32 ARG 0.014 0.001 ARG K 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 323 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.3731 (tp30) cc_final: 0.3498 (mt-10) REVERT: B 90 PHE cc_start: 0.4275 (p90) cc_final: 0.3634 (p90) REVERT: B 207 ARG cc_start: 0.4788 (OUTLIER) cc_final: 0.3144 (ptm160) REVERT: C 106 ARG cc_start: 0.6408 (ptt-90) cc_final: 0.6001 (ptt-90) REVERT: C 113 LYS cc_start: 0.6847 (mtpt) cc_final: 0.6579 (mtmt) REVERT: D 76 TYR cc_start: 0.8061 (t80) cc_final: 0.7821 (t80) REVERT: D 124 MET cc_start: 0.4656 (mtt) cc_final: 0.3835 (mtt) REVERT: E 54 ARG cc_start: 0.7540 (tpt170) cc_final: 0.6800 (mmm-85) REVERT: E 82 GLN cc_start: 0.5401 (OUTLIER) cc_final: 0.4785 (mp10) REVERT: F 10 VAL cc_start: 0.5816 (OUTLIER) cc_final: 0.5595 (m) REVERT: G 30 MET cc_start: -0.1300 (ptt) cc_final: -0.2694 (tmm) REVERT: G 43 TYR cc_start: 0.0958 (OUTLIER) cc_final: 0.0543 (m-10) REVERT: J 80 THR cc_start: 0.4362 (OUTLIER) cc_final: 0.4131 (m) REVERT: K 100 LEU cc_start: 0.6541 (mt) cc_final: 0.6103 (tp) REVERT: K 105 PHE cc_start: 0.4753 (m-80) cc_final: 0.4223 (m-80) REVERT: L 62 GLU cc_start: 0.6410 (mm-30) cc_final: 0.5959 (mm-30) REVERT: L 83 ARG cc_start: 0.5250 (OUTLIER) cc_final: 0.5006 (ptt-90) REVERT: L 103 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6336 (t0) REVERT: M 90 HIS cc_start: 0.1895 (OUTLIER) cc_final: 0.1155 (t-90) REVERT: N 23 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6888 (ptt180) REVERT: N 70 HIS cc_start: 0.6681 (m-70) cc_final: 0.6413 (m-70) REVERT: O 53 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7117 (mmt-90) REVERT: O 56 LEU cc_start: 0.7553 (tt) cc_final: 0.7274 (tp) REVERT: S 19 GLU cc_start: 0.7294 (tm-30) cc_final: 0.5904 (pt0) REVERT: S 65 MET cc_start: 0.1519 (mmt) cc_final: -0.0781 (mtt) REVERT: T 9 LYS cc_start: 0.6351 (OUTLIER) cc_final: 0.5823 (pttp) outliers start: 107 outliers final: 71 residues processed: 393 average time/residue: 0.5824 time to fit residues: 364.5939 Evaluate side-chains 385 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 303 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 22 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 HIS Chi-restraints excluded: chain L residue 83 ARG Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 120 LYS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 23 ARG Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 HIS Chi-restraints excluded: chain O residue 53 ARG Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain S residue 51 HIS Chi-restraints excluded: chain T residue 9 LYS Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 262 optimal weight: 0.0570 chunk 203 optimal weight: 1.9990 chunk 302 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 358 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS D 116 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN M 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5874 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 54842 Z= 0.173 Angle : 0.686 13.677 81524 Z= 0.346 Chirality : 0.038 0.516 10342 Planarity : 0.005 0.080 4723 Dihedral : 24.466 179.549 26209 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.04 % Favored : 90.79 % Rotamer: Outliers : 3.60 % Allowed : 27.74 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.17), residues: 2279 helix: -0.50 (0.17), residues: 845 sheet: -1.88 (0.27), residues: 334 loop : -2.34 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Q 73 HIS 0.013 0.001 HIS L 77 PHE 0.016 0.001 PHE T 51 TYR 0.025 0.002 TYR O 78 ARG 0.015 0.001 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 322 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.3411 (tp30) cc_final: 0.3159 (mt-10) REVERT: B 90 PHE cc_start: 0.3754 (p90) cc_final: 0.3172 (p90) REVERT: B 207 ARG cc_start: 0.4639 (OUTLIER) cc_final: 0.4064 (ptt180) REVERT: C 42 LEU cc_start: 0.6112 (pp) cc_final: 0.5640 (tt) REVERT: C 133 MET cc_start: 0.6561 (pmm) cc_final: 0.6360 (pmm) REVERT: D 76 TYR cc_start: 0.7920 (t80) cc_final: 0.7719 (t80) REVERT: D 124 MET cc_start: 0.4521 (mtt) cc_final: 0.3793 (mtt) REVERT: D 201 VAL cc_start: 0.7459 (t) cc_final: 0.7018 (t) REVERT: E 54 ARG cc_start: 0.7300 (tpt170) cc_final: 0.6581 (mmm-85) REVERT: E 82 GLN cc_start: 0.4951 (OUTLIER) cc_final: 0.4275 (mp10) REVERT: H 10 MET cc_start: 0.5255 (ttp) cc_final: 0.4414 (tpt) REVERT: K 100 LEU cc_start: 0.6080 (mt) cc_final: 0.5836 (tp) REVERT: L 62 GLU cc_start: 0.6306 (mm-30) cc_final: 0.5900 (mm-30) REVERT: N 26 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5537 (tp) REVERT: N 70 HIS cc_start: 0.6687 (m-70) cc_final: 0.6328 (m-70) REVERT: O 56 LEU cc_start: 0.7680 (tt) cc_final: 0.7382 (tp) REVERT: O 67 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6326 (mt) REVERT: S 19 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6163 (pt0) REVERT: S 65 MET cc_start: 0.1406 (mmt) cc_final: -0.1304 (mtt) REVERT: T 36 TYR cc_start: 0.6202 (m-80) cc_final: 0.5646 (m-80) outliers start: 69 outliers final: 49 residues processed: 373 average time/residue: 0.5828 time to fit residues: 344.3967 Evaluate side-chains 347 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 294 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 22 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 104 ASN Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 HIS Chi-restraints excluded: chain O residue 67 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 281 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 GLN D 131 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 119 ASN L 77 HIS M 104 ASN N 48 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 54842 Z= 0.495 Angle : 1.154 15.369 81524 Z= 0.568 Chirality : 0.056 0.500 10342 Planarity : 0.009 0.094 4723 Dihedral : 25.304 179.613 26209 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 32.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.44 % Favored : 85.30 % Rotamer: Outliers : 6.47 % Allowed : 26.12 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.16), residues: 2279 helix: -1.53 (0.16), residues: 840 sheet: -2.30 (0.27), residues: 330 loop : -2.98 (0.16), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP Q 73 HIS 0.017 0.003 HIS T 20 PHE 0.044 0.004 PHE C 28 TYR 0.042 0.005 TYR K 77 ARG 0.022 0.001 ARG M 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 321 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 90 PHE cc_start: 0.4327 (p90) cc_final: 0.3493 (p90) REVERT: C 129 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.4736 (p90) REVERT: D 124 MET cc_start: 0.4878 (mtt) cc_final: 0.4404 (mtt) REVERT: E 11 LEU cc_start: 0.6238 (pp) cc_final: 0.5993 (pt) REVERT: E 54 ARG cc_start: 0.7633 (tpt170) cc_final: 0.6823 (mmm160) REVERT: E 82 GLN cc_start: 0.5858 (OUTLIER) cc_final: 0.5224 (mp10) REVERT: F 10 VAL cc_start: 0.5401 (OUTLIER) cc_final: 0.5192 (m) REVERT: G 30 MET cc_start: -0.0688 (OUTLIER) cc_final: -0.2310 (tmm) REVERT: G 43 TYR cc_start: 0.1187 (OUTLIER) cc_final: 0.0523 (m-10) REVERT: H 10 MET cc_start: 0.5869 (ttp) cc_final: 0.4574 (tpp) REVERT: I 56 MET cc_start: 0.0122 (ptt) cc_final: -0.0394 (ttp) REVERT: K 76 GLU cc_start: 0.5040 (OUTLIER) cc_final: 0.3392 (tm-30) REVERT: L 103 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6254 (t0) REVERT: M 104 ASN cc_start: 0.5099 (OUTLIER) cc_final: 0.4410 (t0) REVERT: N 23 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6680 (ppt170) REVERT: O 56 LEU cc_start: 0.7528 (tt) cc_final: 0.7283 (tp) REVERT: P 35 ARG cc_start: 0.7651 (tpt-90) cc_final: 0.7437 (tpt-90) REVERT: S 19 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6010 (pt0) REVERT: S 65 MET cc_start: 0.2285 (mmt) cc_final: 0.1576 (mpp) outliers start: 124 outliers final: 87 residues processed: 407 average time/residue: 0.5778 time to fit residues: 378.1251 Evaluate side-chains 396 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 300 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 192 TYR Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 30 MET Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 22 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 24 HIS Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 77 HIS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 104 ASN Chi-restraints excluded: chain N residue 23 ARG Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 35 GLN Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 HIS Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 51 ASN Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 68 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 51 HIS Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 334 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 301 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS D 116 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 54842 Z= 0.204 Angle : 0.754 14.058 81524 Z= 0.382 Chirality : 0.041 0.507 10342 Planarity : 0.006 0.084 4723 Dihedral : 24.744 179.275 26209 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.87 % Favored : 89.91 % Rotamer: Outliers : 3.81 % Allowed : 29.04 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.16), residues: 2279 helix: -0.90 (0.17), residues: 847 sheet: -2.13 (0.26), residues: 345 loop : -2.65 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP Q 73 HIS 0.010 0.001 HIS L 77 PHE 0.031 0.002 PHE C 28 TYR 0.031 0.002 TYR O 78 ARG 0.018 0.001 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 327 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.3640 (tp30) cc_final: 0.3275 (mt-10) REVERT: C 42 LEU cc_start: 0.5947 (pp) cc_final: 0.5662 (mt) REVERT: D 76 TYR cc_start: 0.7935 (t80) cc_final: 0.7668 (t80) REVERT: D 201 VAL cc_start: 0.7472 (t) cc_final: 0.7043 (t) REVERT: E 11 LEU cc_start: 0.5972 (pp) cc_final: 0.5716 (pt) REVERT: E 54 ARG cc_start: 0.7389 (tpt170) cc_final: 0.6632 (mmm-85) REVERT: E 64 MET cc_start: 0.7448 (tpp) cc_final: 0.7117 (tpp) REVERT: E 82 GLN cc_start: 0.5192 (OUTLIER) cc_final: 0.4531 (mp10) REVERT: F 21 MET cc_start: 0.3984 (mtm) cc_final: 0.3635 (mtm) REVERT: F 39 LEU cc_start: 0.7283 (mt) cc_final: 0.7004 (pp) REVERT: F 102 MET cc_start: 0.6870 (mpp) cc_final: 0.6617 (mpp) REVERT: H 10 MET cc_start: 0.5331 (ttp) cc_final: 0.4384 (tpp) REVERT: I 56 MET cc_start: -0.0658 (ptt) cc_final: -0.1194 (ttp) REVERT: K 76 GLU cc_start: 0.4681 (OUTLIER) cc_final: 0.3084 (tm-30) REVERT: N 23 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6596 (ptt180) REVERT: O 56 LEU cc_start: 0.7749 (tt) cc_final: 0.7483 (tp) REVERT: P 1 MET cc_start: 0.3873 (mmt) cc_final: 0.2615 (mmt) REVERT: S 19 GLU cc_start: 0.7252 (tm-30) cc_final: 0.5939 (pt0) REVERT: S 65 MET cc_start: 0.3173 (mmt) cc_final: 0.2147 (mpp) REVERT: T 36 TYR cc_start: 0.6347 (m-80) cc_final: 0.5764 (m-80) outliers start: 73 outliers final: 56 residues processed: 376 average time/residue: 0.5697 time to fit residues: 340.7548 Evaluate side-chains 368 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 309 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 143 MET Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 22 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 77 HIS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 23 ARG Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 HIS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.7980 chunk 353 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 chunk 245 optimal weight: 0.8980 chunk 370 optimal weight: 5.9990 chunk 341 optimal weight: 7.9990 chunk 295 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 227 optimal weight: 0.0870 chunk 180 optimal weight: 3.9990 overall best weight: 2.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS C 31 ASN D 116 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 HIS ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5990 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 54842 Z= 0.207 Angle : 0.742 13.819 81524 Z= 0.374 Chirality : 0.040 0.498 10342 Planarity : 0.006 0.089 4723 Dihedral : 24.646 179.410 26209 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.15 % Favored : 88.59 % Rotamer: Outliers : 3.44 % Allowed : 29.77 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.16), residues: 2279 helix: -0.73 (0.17), residues: 837 sheet: -1.99 (0.26), residues: 345 loop : -2.54 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Q 73 HIS 0.034 0.002 HIS C 189 PHE 0.022 0.002 PHE C 28 TYR 0.045 0.002 TYR G 43 ARG 0.018 0.001 ARG D 62 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4558 Ramachandran restraints generated. 2279 Oldfield, 0 Emsley, 2279 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 322 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 GLU cc_start: 0.3394 (tp30) cc_final: 0.3046 (mt-10) REVERT: B 90 PHE cc_start: 0.4016 (p90) cc_final: 0.3339 (p90) REVERT: C 42 LEU cc_start: 0.5923 (pp) cc_final: 0.5436 (mt) REVERT: C 129 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.4569 (p90) REVERT: D 8 LYS cc_start: 0.8026 (mttp) cc_final: 0.7473 (mtpt) REVERT: D 201 VAL cc_start: 0.7452 (t) cc_final: 0.7202 (t) REVERT: E 11 LEU cc_start: 0.5861 (pp) cc_final: 0.5573 (pt) REVERT: E 54 ARG cc_start: 0.7360 (tpt170) cc_final: 0.6609 (mmm-85) REVERT: E 64 MET cc_start: 0.7503 (tpp) cc_final: 0.7171 (tpp) REVERT: E 82 GLN cc_start: 0.5095 (OUTLIER) cc_final: 0.4449 (mp10) REVERT: F 102 MET cc_start: 0.6680 (mpp) cc_final: 0.6335 (mpp) REVERT: H 10 MET cc_start: 0.5498 (ttp) cc_final: 0.4420 (tpp) REVERT: I 56 MET cc_start: -0.0224 (ptt) cc_final: -0.0740 (ttp) REVERT: K 76 GLU cc_start: 0.4745 (OUTLIER) cc_final: 0.3254 (tm-30) REVERT: M 90 HIS cc_start: 0.1315 (OUTLIER) cc_final: 0.0549 (t-90) REVERT: N 23 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6667 (ptt180) REVERT: O 56 LEU cc_start: 0.7742 (tt) cc_final: 0.7518 (tp) REVERT: P 1 MET cc_start: 0.4258 (mmt) cc_final: 0.2884 (mmt) REVERT: S 65 MET cc_start: 0.3356 (mmt) cc_final: 0.2232 (mpp) REVERT: T 36 TYR cc_start: 0.6202 (m-80) cc_final: 0.5569 (m-80) REVERT: T 48 GLN cc_start: 0.6879 (tm-30) cc_final: 0.6421 (tm-30) outliers start: 66 outliers final: 55 residues processed: 366 average time/residue: 0.5971 time to fit residues: 345.3207 Evaluate side-chains 369 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 309 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 83 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 169 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 3 MET Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 111 MET Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 22 HIS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 77 HIS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 90 HIS Chi-restraints excluded: chain N residue 23 ARG Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 76 PHE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 50 HIS Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain R residue 28 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 31 ARG Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain T residue 75 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 1.9990 chunk 314 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 272 optimal weight: 0.0040 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 295 optimal weight: 0.0070 chunk 123 optimal weight: 10.0000 chunk 303 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 2.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS D 116 GLN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.178961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.167313 restraints weight = 174997.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.169444 restraints weight = 80431.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.170778 restraints weight = 44265.961| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 54842 Z= 0.232 Angle : 0.765 14.277 81524 Z= 0.385 Chirality : 0.041 0.506 10342 Planarity : 0.006 0.091 4723 Dihedral : 24.654 179.938 26209 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.10 % Favored : 88.68 % Rotamer: Outliers : 3.91 % Allowed : 29.51 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.17), residues: 2279 helix: -0.76 (0.17), residues: 838 sheet: -2.06 (0.26), residues: 347 loop : -2.51 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Q 73 HIS 0.014 0.001 HIS L 77 PHE 0.031 0.002 PHE C 28 TYR 0.040 0.003 TYR G 43 ARG 0.015 0.001 ARG P 28 =============================================================================== Job complete usr+sys time: 7888.48 seconds wall clock time: 139 minutes 50.12 seconds (8390.12 seconds total)