Starting phenix.real_space_refine (version: dev) on Sat Apr 9 21:42:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/04_2022/6w7m_21571.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/04_2022/6w7m_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_21571/04_2022/6w7m_21571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/04_2022/6w7m_21571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/04_2022/6w7m_21571.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w7m_21571/04_2022/6w7m_21571.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'rna3p_pyr': 565, 'rna2p_pur': 114, 'rna3p_pur': 749, 'rna2p_pyr': 84} Link IDs: {'rna3p': 1314, 'rna2p': 197} 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: {'PTRANS': 6, 'TRANS': 114, 'PCIS': 1} 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: 27.63, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 24.14 Conformation dependent library (CDL) restraints added in 3.0 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: 19.76 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: 44.36 Time building geometry restraints manager: 25.91 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: 98.29 - 106.13: 8680 106.13 - 113.97: 34706 113.97 - 121.81: 25496 121.81 - 129.65: 11666 129.65 - 137.49: 976 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: 28205 35.74 - 71.49: 1290 71.49 - 107.23: 101 107.23 - 142.98: 13 142.98 - 178.72: 14 Dihedral angle restraints: 29623 sinusoidal: 22980 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 29620 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 2.440 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 2.440 nonbonded pdb=" O2' A A1374 " pdb=" O ASN G 27 " model vdw 2.107 2.440 ... (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 ========== 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 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: 0.040 Extract box with map and model: 10.920 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.390 Process input model: 160.950 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 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 : 16.556 178.724 25329 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 % 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 *********************** 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 : 3.523 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 outliers start: 2 outliers final: 0 residues processed: 528 average time/residue: 0.7558 time to fit residues: 609.3225 Evaluate side-chains 344 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 344 time to evaluate : 3.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4987 ------------------------------------------------------------------------------- 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: 10.0000 chunk 281 optimal weight: 1.9990 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 291 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 177 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 337 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 119 GLN B 145 ASN ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN C 139 ASN C 175 HIS C 189 HIS D 41 HIS D 74 ASN ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN E 70 ASN ** F 3 HIS ** 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** I 125 GLN J 58 ASN K 40 ASN K 118 HIS L 77 HIS M 99 GLN M 104 ASN N 48 GLN N 59 GLN O 28 GLN O 46 HIS P 9 HIS P 63 GLN S 51 HIS S 56 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN T 68 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 54842 Z= 0.270 Angle : 0.773 15.833 81524 Z= 0.388 Chirality : 0.040 0.483 10342 Planarity : 0.006 0.088 4723 Dihedral : 16.799 177.863 20721 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.40 % Favored : 89.38 % Rotamer Outliers : 3.39 % 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: -3.13 (0.16), residues: 2279 helix: -1.20 (0.16), residues: 831 sheet: -2.13 (0.25), residues: 350 loop : -2.77 (0.17), residues: 1098 *********************** 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: 65 poor density : 379 time to evaluate : 3.259 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 outliers start: 65 outliers final: 39 residues processed: 413 average time/residue: 0.7184 time to fit residues: 466.3685 Evaluate side-chains 363 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 324 time to evaluate : 3.137 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4623 time to fit residues: 37.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 230 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 365 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 335 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 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** I 125 GLN J 20 GLN K 29 ASN K 109 ASN L 6 GLN L 96 HIS M 99 GLN ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 GLN O 35 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 54842 Z= 0.333 Angle : 0.897 11.788 81524 Z= 0.453 Chirality : 0.047 0.450 10342 Planarity : 0.008 0.122 4723 Dihedral : 17.700 178.708 20721 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 30.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.94 % Favored : 87.80 % Rotamer Outliers : 4.43 % 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: -3.28 (0.16), residues: 2279 helix: -1.35 (0.16), residues: 828 sheet: -2.06 (0.27), residues: 313 loop : -2.90 (0.17), residues: 1138 *********************** 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 435 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 350 time to evaluate : 3.437 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 outliers start: 85 outliers final: 48 residues processed: 408 average time/residue: 0.7049 time to fit residues: 464.4941 Evaluate side-chains 356 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 308 time to evaluate : 3.229 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.5186 time to fit residues: 48.9419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 339 optimal weight: 0.7980 chunk 359 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 321 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** J 58 ASN ** O 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 54842 Z= 0.224 Angle : 0.734 17.475 81524 Z= 0.373 Chirality : 0.040 0.489 10342 Planarity : 0.006 0.120 4723 Dihedral : 17.265 178.577 20721 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.32 % Favored : 88.42 % Rotamer Outliers : 2.97 % 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: -2.79 (0.16), residues: 2279 helix: -0.86 (0.17), residues: 847 sheet: -2.01 (0.27), residues: 341 loop : -2.62 (0.18), residues: 1091 *********************** 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 381 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 324 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 30 residues processed: 361 average time/residue: 0.7195 time to fit residues: 412.7151 Evaluate side-chains 323 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 293 time to evaluate : 3.225 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5131 time to fit residues: 30.8758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 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: 8.9990 chunk 322 optimal weight: 0.0370 chunk 90 optimal weight: 8.9990 overall best weight: 2.2062 ------------------------------------------------------------------------------- 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** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN D 131 ASN ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 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 96 HIS O 38 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6030 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.113 54842 Z= 0.211 Angle : 0.711 16.141 81524 Z= 0.359 Chirality : 0.039 0.481 10342 Planarity : 0.006 0.107 4723 Dihedral : 17.126 179.021 20721 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 11.19 % Favored : 88.55 % Rotamer Outliers : 2.97 % 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: -2.56 (0.17), residues: 2279 helix: -0.70 (0.17), residues: 854 sheet: -1.86 (0.27), residues: 329 loop : -2.49 (0.18), residues: 1096 *********************** 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 377 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 320 time to evaluate : 3.147 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 outliers start: 57 outliers final: 24 residues processed: 358 average time/residue: 0.6887 time to fit residues: 394.8502 Evaluate side-chains 314 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 290 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4748 time to fit residues: 24.2703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 71 optimal weight: 9.9990 chunk 211 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 359 optimal weight: 0.0570 chunk 298 optimal weight: 2.9990 chunk 166 optimal weight: 0.0050 chunk 29 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 0.8980 overall best weight: 1.5916 ------------------------------------------------------------------------------- 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** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** L 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN T 52 ASN ** T 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5984 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.177 54842 Z= 0.188 Angle : 0.663 12.542 81524 Z= 0.335 Chirality : 0.037 0.492 10342 Planarity : 0.006 0.118 4723 Dihedral : 16.939 179.514 20721 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 10.62 % Favored : 89.12 % Rotamer Outliers : 1.82 % 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: -2.30 (0.17), residues: 2279 helix: -0.46 (0.17), residues: 865 sheet: -1.79 (0.27), residues: 330 loop : -2.35 (0.18), residues: 1084 *********************** 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 357 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 322 time to evaluate : 3.174 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 outliers start: 35 outliers final: 15 residues processed: 342 average time/residue: 0.7190 time to fit residues: 391.5430 Evaluate side-chains 311 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 296 time to evaluate : 3.281 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.5391 time to fit residues: 17.2375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 0.5980 chunk 40 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 262 optimal weight: 0.9980 chunk 203 optimal weight: 0.0030 chunk 302 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 358 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 218 optimal weight: 0.0050 chunk 165 optimal weight: 10.0000 overall best weight: 0.5204 ------------------------------------------------------------------------------- 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** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 HIS D 131 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS J 58 ASN J 64 GLN K 38 GLN L 5 ASN O 35 GLN T 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.322 54842 Z= 0.207 Angle : 0.633 21.121 81524 Z= 0.321 Chirality : 0.034 0.485 10342 Planarity : 0.006 0.117 4723 Dihedral : 16.507 179.132 20721 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.86 % Favored : 90.87 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.96 (0.17), residues: 2279 helix: -0.22 (0.18), residues: 870 sheet: -1.59 (0.28), residues: 335 loop : -2.12 (0.18), residues: 1074 *********************** 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 363 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 337 time to evaluate : 3.354 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 outliers start: 26 outliers final: 11 residues processed: 348 average time/residue: 0.7193 time to fit residues: 401.9010 Evaluate side-chains 310 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 299 time to evaluate : 3.134 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4707 time to fit residues: 13.0869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 214 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 244 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** D 36 GLN D 131 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.312 54842 Z= 0.469 Angle : 1.107 13.887 81524 Z= 0.553 Chirality : 0.054 0.499 10342 Planarity : 0.009 0.138 4723 Dihedral : 18.445 179.289 20721 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 38.68 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.00 % Favored : 85.56 % Rotamer Outliers : 3.18 % 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: -3.21 (0.16), residues: 2279 helix: -1.38 (0.16), residues: 833 sheet: -2.00 (0.27), residues: 340 loop : -2.78 (0.17), residues: 1106 *********************** 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 381 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 320 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 41 residues processed: 356 average time/residue: 0.6806 time to fit residues: 387.3459 Evaluate side-chains 337 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 296 time to evaluate : 3.207 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4729 time to fit residues: 39.1169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 5.9990 chunk 343 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 chunk 201 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 262 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 chunk 332 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 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** J 58 ASN ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN N 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 1.011 54842 Z= 0.636 Angle : 1.122 83.463 81524 Z= 0.549 Chirality : 0.050 0.493 10342 Planarity : 0.009 0.157 4723 Dihedral : 18.316 179.489 20721 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 34.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.22 % Favored : 85.52 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.09 % 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: -3.30 (0.16), residues: 2279 helix: -1.47 (0.16), residues: 842 sheet: -2.02 (0.27), residues: 331 loop : -2.83 (0.17), residues: 1106 *********************** 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 336 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 305 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 321 average time/residue: 0.6923 time to fit residues: 354.2299 Evaluate side-chains 306 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 292 time to evaluate : 3.056 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5035 time to fit residues: 16.0044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 2.9990 chunk 353 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 370 optimal weight: 0.0870 chunk 341 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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** D 131 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 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 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.977 54842 Z= 0.609 Angle : 1.086 93.053 81524 Z= 0.530 Chirality : 0.048 0.613 10342 Planarity : 0.009 0.190 4723 Dihedral : 18.169 179.337 20721 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 31.29 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.95 % Favored : 85.70 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.09 % 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: -3.19 (0.16), residues: 2279 helix: -1.36 (0.16), residues: 838 sheet: -2.01 (0.28), residues: 325 loop : -2.78 (0.17), residues: 1116 ********************** 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 309 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 298 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 303 average time/residue: 0.6953 time to fit residues: 338.0797 Evaluate side-chains 297 residues out of total 1918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 290 time to evaluate : 3.175 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6695 time to fit residues: 11.1611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 295 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 303 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.175098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.163584 restraints weight = 179485.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.165618 restraints weight = 83222.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.166876 restraints weight = 46133.658| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.925 54842 Z= 0.647 Angle : 1.093 76.925 81524 Z= 0.540 Chirality : 0.050 0.512 10342 Planarity : 0.009 0.143 4723 Dihedral : 18.155 179.136 20721 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 32.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.95 % Favored : 85.70 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 1.22 % 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: -3.21 (0.16), residues: 2279 helix: -1.34 (0.16), residues: 838 sheet: -2.05 (0.28), residues: 325 loop : -2.80 (0.17), residues: 1116 =============================================================================== Job complete usr+sys time: 8455.43 seconds wall clock time: 157 minutes 1.74 seconds (9421.74 seconds total)