Starting phenix.real_space_refine (version: dev) on Wed May 18 07:56:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/05_2022/6zok_11321.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/05_2022/6zok_11321.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/05_2022/6zok_11321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/05_2022/6zok_11321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/05_2022/6zok_11321.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zok_11321/05_2022/6zok_11321.pdb" } resolution = 2.8 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= -0.002 sd= 0.143 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 50192 Number of models: 1 Model: "" Number of chains: 26 Chain: "2" Number of atoms: 26317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1232, 26317 Classifications: {'RNA': 1232} Modifications used: {'rna3p_pyr': 500, 'rna2p_pur': 97, 'rna3p_pur': 564, 'rna2p_pyr': 71} Link IDs: {'rna3p': 1063, 'rna2p': 168} Chain breaks: 6 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "C" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1690 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1010 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "R" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 397 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 125, 'PCIS': 2} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 135, 'PCIS': 1} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "e" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 441 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "j" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 267 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "h" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "2" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Unusual residues: {' MG': 106} Classifications: {'undetermined': 106} Link IDs: {None: 105} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 47859 SG CYS a 23 117.904 51.954 131.049 1.00 7.83 S ATOM 47880 SG CYS a 26 114.787 50.718 129.391 1.00 8.94 S ATOM 48263 SG CYS a 74 114.688 53.990 131.361 1.00 8.19 S ATOM 48282 SG CYS a 77 114.887 50.761 133.067 1.00 8.63 S Time building chain proxies: 27.88, per 1000 atoms: 0.56 Number of scatterers: 50192 At special positions: 0 Unit cell: (181.44, 189, 201.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 106 16.00 P 1232 15.00 Mg 109 11.99 O 12722 8.00 N 9246 7.00 C 26776 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 40 " - pdb=" SG CYS b 59 " distance=2.03 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: 22.18 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 26 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 74 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " Number of angles added : 6 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 32 sheets defined 36.2% alpha, 20.0% beta 340 base pairs and 645 stacking pairs defined. Time for finding SS restraints: 20.53 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 80 through 95 removed outlier: 3.688A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.840A pdb=" N SER A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.543A pdb=" N TYR A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.564A pdb=" N ILE A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 26 Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 72 through 74 No H-bonds generated for 'chain 'B' and resid 72 through 74' Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.655A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 77 through 84 removed outlier: 4.027A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.561A pdb=" N ASP C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.579A pdb=" N LEU C 102 " --> pdb=" O GLY C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 146 through 161 Processing helix chain 'C' and resid 207 through 218 removed outlier: 3.836A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.526A pdb=" N TRP C 256 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.505A pdb=" N MET E 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.976A pdb=" N CYS E 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.567A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 119 No H-bonds generated for 'chain 'E' and resid 117 through 119' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 247 through 261 Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.676A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR G 26 " --> pdb=" O ARG G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.822A pdb=" N LYS G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 34 Processing helix chain 'H' and resid 36 through 43 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 87 removed outlier: 3.617A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG H 78 " --> pdb=" O LYS H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.780A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.808A pdb=" N VAL H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 130 through 138 Processing helix chain 'I' and resid 142 through 153 Processing helix chain 'I' and resid 159 through 169 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 192 through 206 Processing helix chain 'J' and resid 21 through 36 Processing helix chain 'J' and resid 40 through 61 removed outlier: 3.592A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.566A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.823A pdb=" N MET J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.786A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 153 through 155 No H-bonds generated for 'chain 'J' and resid 153 through 155' Processing helix chain 'J' and resid 171 through 181 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.610A pdb=" N THR L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 Processing helix chain 'N' and resid 29 through 44 Processing helix chain 'N' and resid 46 through 58 Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 removed outlier: 4.084A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 132 Processing helix chain 'N' and resid 142 through 150 removed outlier: 4.240A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA N 148 " --> pdb=" O SER N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 66 through 69 removed outlier: 4.294A pdb=" N SER O 69 " --> pdb=" O ARG O 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 66 through 69' Processing helix chain 'O' and resid 70 through 89 Processing helix chain 'O' and resid 111 through 122 Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'V' and resid 56 through 63 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.757A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.745A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 removed outlier: 3.714A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 120 Processing helix chain 'X' and resid 9 through 21 Processing helix chain 'X' and resid 24 through 33 removed outlier: 4.462A pdb=" N GLY X 33 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 39 Processing helix chain 'X' and resid 89 through 94 removed outlier: 3.518A pdb=" N ASN X 92 " --> pdb=" O GLY X 89 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 49 Processing helix chain 'Y' and resid 51 through 53 No H-bonds generated for 'chain 'Y' and resid 51 through 53' Processing helix chain 'Y' and resid 78 through 86 Processing helix chain 'Y' and resid 87 through 94 removed outlier: 3.592A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 114 Processing helix chain 'Y' and resid 119 through 125 Processing helix chain 'a' and resid 46 through 57 removed outlier: 3.665A pdb=" N ARG a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU a 55 " --> pdb=" O ARG a 51 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA a 56 " --> pdb=" O ASP a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'b' and resid 11 through 18 Processing helix chain 'e' and resid 30 through 42 Processing helix chain 'j' and resid 152 through 161 Processing helix chain 'j' and resid 165 through 179 removed outlier: 3.506A pdb=" N GLY j 179 " --> pdb=" O ARG j 175 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 21 Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.012A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.736A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 122 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N LEU A 147 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 124 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA A 146 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.238A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 50 removed outlier: 4.238A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 13.359A pdb=" N ASN B 99 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 13.137A pdb=" N LYS B 219 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N HIS B 101 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET B 217 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N ARG B 213 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N PHE B 211 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N PHE B 142 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG B 213 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N VAL B 140 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 219 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 115 removed outlier: 6.609A pdb=" N PHE C 127 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C 109 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS C 125 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG C 123 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLN C 113 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ARG C 121 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 188 Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AA8, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.576A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.080A pdb=" N ILE E 136 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N VAL E 131 " --> pdb=" O ILE E 136 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.880A pdb=" N ASN E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.361A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL G 112 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE G 52 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL G 114 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL G 50 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB5, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 53 removed outlier: 6.815A pdb=" N LYS H 58 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.361A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY H 141 " --> pdb=" O HIS H 157 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.346A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.233A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 62 through 67 removed outlier: 6.030A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP I 105 " --> pdb=" O ARG I 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AC3, first strand: chain 'L' and resid 72 through 82 removed outlier: 16.839A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.843A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS L 81 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.823A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AC6, first strand: chain 'V' and resid 32 through 39 removed outlier: 6.633A pdb=" N ILE V 32 " --> pdb=" O TYR V 53 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TYR V 53 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N MET V 34 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS V 51 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL V 36 " --> pdb=" O GLN V 49 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLN V 49 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLU V 38 " --> pdb=" O ASN V 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AC8, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.591A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.500A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N PHE X 120 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR X 82 " --> pdb=" O PHE X 120 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL X 122 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N PHE X 84 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N LYS X 124 " --> pdb=" O PHE X 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.289A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AD3, first strand: chain 'a' and resid 36 through 43 Processing sheet with id=AD4, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AD5, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.703A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 858 hydrogen bonds 1388 hydrogen bond angles 0 basepair planarities 340 basepair parallelities 645 stacking parallelities Total time for adding SS restraints: 47.01 Time building geometry restraints manager: 23.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11480 1.34 - 1.46: 18664 1.46 - 1.58: 20838 1.58 - 1.70: 2457 1.70 - 1.83: 164 Bond restraints: 53603 Sorted by residual: bond pdb=" N GLU G 118 " pdb=" CA GLU G 118 " ideal model delta sigma weight residual 1.459 1.475 -0.017 1.16e-02 7.43e+03 2.11e+00 bond pdb=" N GLY G 117 " pdb=" CA GLY G 117 " ideal model delta sigma weight residual 1.445 1.455 -0.011 9.20e-03 1.18e+04 1.34e+00 bond pdb=" N1 C 21717 " pdb=" C2 C 21717 " ideal model delta sigma weight residual 1.397 1.418 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" CA TYR E 149 " pdb=" CB TYR E 149 " ideal model delta sigma weight residual 1.522 1.530 -0.007 7.00e-03 2.04e+04 1.09e+00 bond pdb=" N PRO A 207 " pdb=" CA PRO A 207 " ideal model delta sigma weight residual 1.469 1.481 -0.012 1.28e-02 6.10e+03 9.44e-01 ... (remaining 53598 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.98: 7793 106.98 - 113.75: 31984 113.75 - 120.53: 20349 120.53 - 127.30: 15430 127.30 - 134.07: 2702 Bond angle restraints: 78258 Sorted by residual: angle pdb=" N GLU X 53 " pdb=" CA GLU X 53 " pdb=" C GLU X 53 " ideal model delta sigma weight residual 107.88 113.44 -5.56 1.41e+00 5.03e-01 1.55e+01 angle pdb=" C PRO H 65 " pdb=" N VAL H 66 " pdb=" CA VAL H 66 " ideal model delta sigma weight residual 120.33 123.11 -2.78 8.00e-01 1.56e+00 1.21e+01 angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" C1' C 2 501 " pdb=" N1 C 2 501 " pdb=" C2 C 2 501 " ideal model delta sigma weight residual 118.80 127.98 -9.18 3.00e+00 1.11e-01 9.36e+00 angle pdb=" C2' U 2 918 " pdb=" C1' U 2 918 " pdb=" N1 U 2 918 " ideal model delta sigma weight residual 112.00 116.28 -4.28 1.50e+00 4.44e-01 8.13e+00 ... (remaining 78253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 28846 35.97 - 71.94: 862 71.94 - 107.91: 80 107.91 - 143.88: 5 143.88 - 179.85: 13 Dihedral angle restraints: 29806 sinusoidal: 21275 harmonic: 8531 Sorted by residual: dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual 200.00 28.65 171.35 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual -160.00 7.61 -167.61 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' C 2 853 " pdb=" C1' C 2 853 " pdb=" N1 C 2 853 " pdb=" C2 C 2 853 " ideal model delta sinusoidal sigma weight residual -160.00 -1.87 -158.13 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 29803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 8541 0.049 - 0.097: 918 0.097 - 0.146: 253 0.146 - 0.195: 12 0.195 - 0.244: 4 Chirality restraints: 9728 Sorted by residual: chirality pdb=" C1' U 2 918 " pdb=" O4' U 2 918 " pdb=" C2' U 2 918 " pdb=" N1 U 2 918 " both_signs ideal model delta sigma weight residual False 2.47 2.22 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1' G 2 470 " pdb=" O4' G 2 470 " pdb=" C2' G 2 470 " pdb=" N9 G 2 470 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1' G 2 659 " pdb=" O4' G 2 659 " pdb=" C2' G 2 659 " pdb=" N9 G 2 659 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 9725 not shown) Planarity restraints: 5356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 2 60 " 0.032 2.00e-02 2.50e+03 1.44e-02 5.67e+00 pdb=" N9 A 2 60 " -0.033 2.00e-02 2.50e+03 pdb=" C8 A 2 60 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A 2 60 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A 2 60 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 2 60 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A 2 60 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A 2 60 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 2 60 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 2 60 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A 2 60 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 669 " -0.031 2.00e-02 2.50e+03 1.40e-02 5.40e+00 pdb=" N9 A 2 669 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A 2 669 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A 2 669 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 2 669 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A 2 669 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 2 669 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 2 669 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 2 669 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A 2 669 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A 2 669 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 918 " 0.029 2.00e-02 2.50e+03 1.53e-02 5.26e+00 pdb=" N1 U 2 918 " -0.034 2.00e-02 2.50e+03 pdb=" C2 U 2 918 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U 2 918 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U 2 918 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U 2 918 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U 2 918 " 0.010 2.00e-02 2.50e+03 pdb=" C5 U 2 918 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U 2 918 " -0.006 2.00e-02 2.50e+03 ... (remaining 5353 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 317 2.57 - 3.15: 35949 3.15 - 3.74: 87893 3.74 - 4.32: 129074 4.32 - 4.90: 181667 Nonbonded interactions: 434900 Sorted by model distance: nonbonded pdb=" OP1 G 21837 " pdb="MG MG 21936 " model vdw 1.989 2.170 nonbonded pdb=" N4 C 21842 " pdb="MG MG 21915 " model vdw 2.003 2.250 nonbonded pdb=" OP2 U 2 100 " pdb="MG MG 21920 " model vdw 2.034 2.170 nonbonded pdb=" OP2 A 2 594 " pdb="MG MG 21962 " model vdw 2.044 2.170 nonbonded pdb=" OE1 GLN G 177 " pdb="MG MG 22004 " model vdw 2.063 2.170 ... (remaining 434895 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1232 5.49 5 Mg 109 5.21 5 S 106 5.16 5 C 26776 2.51 5 N 9246 2.21 5 O 12722 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 46.110 Check model and map are aligned: 0.820 Convert atoms to be neutral: 0.430 Process input model: 173.150 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.170 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 245.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 : 0.003 0.029 53603 Z= 0.156 Angle : 0.521 9.177 78258 Z= 0.288 Chirality : 0.034 0.244 9728 Planarity : 0.004 0.052 5356 Dihedral : 14.363 179.848 24295 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.55 (0.15), residues: 2928 helix: 1.31 (0.17), residues: 937 sheet: 0.09 (0.21), residues: 562 loop : -0.05 (0.16), residues: 1429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 485 time to evaluate : 4.048 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 11 residues processed: 515 average time/residue: 1.8677 time to fit residues: 1172.4474 Evaluate side-chains 390 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 379 time to evaluate : 3.783 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 3 average time/residue: 1.0678 time to fit residues: 8.9164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 210 optimal weight: 0.4980 chunk 166 optimal weight: 4.9990 chunk 322 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 374 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS A 141 ASN C 113 GLN ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 146 GLN L 39 ASN O 83 GLN W 56 HIS X 61 GLN Y 106 GLN a 43 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 53603 Z= 0.440 Angle : 0.705 11.140 78258 Z= 0.358 Chirality : 0.045 0.273 9728 Planarity : 0.006 0.071 5356 Dihedral : 15.022 178.758 18065 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.30 (0.15), residues: 2928 helix: 1.12 (0.17), residues: 959 sheet: 0.02 (0.21), residues: 560 loop : -0.28 (0.16), residues: 1409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 378 time to evaluate : 3.803 Fit side-chains outliers start: 97 outliers final: 45 residues processed: 434 average time/residue: 1.8247 time to fit residues: 971.3402 Evaluate side-chains 411 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 366 time to evaluate : 3.893 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 32 residues processed: 14 average time/residue: 0.6558 time to fit residues: 19.4252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 311 optimal weight: 4.9990 chunk 254 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 chunk 404 optimal weight: 0.9990 chunk 333 optimal weight: 6.9990 chunk 371 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 300 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 186 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN L 39 ASN O 83 GLN O 103 ASN V 49 GLN a 43 ASN b 19 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 53603 Z= 0.176 Angle : 0.532 10.634 78258 Z= 0.275 Chirality : 0.036 0.254 9728 Planarity : 0.004 0.051 5356 Dihedral : 14.871 178.110 18065 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.59 (0.15), residues: 2928 helix: 1.50 (0.17), residues: 960 sheet: 0.10 (0.21), residues: 549 loop : -0.18 (0.16), residues: 1419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 378 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 49 residues processed: 432 average time/residue: 1.8110 time to fit residues: 962.2850 Evaluate side-chains 409 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 360 time to evaluate : 3.821 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 32 residues processed: 17 average time/residue: 0.7940 time to fit residues: 24.6531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 0.9980 chunk 281 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 376 optimal weight: 7.9990 chunk 398 optimal weight: 10.0000 chunk 196 optimal weight: 0.0270 chunk 356 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 HIS H 76 GLN H 186 ASN I 99 ASN I 167 GLN O 103 ASN V 47 ASN a 43 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 53603 Z= 0.210 Angle : 0.543 11.292 78258 Z= 0.280 Chirality : 0.037 0.257 9728 Planarity : 0.004 0.053 5356 Dihedral : 14.811 178.184 18065 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.66 (0.15), residues: 2928 helix: 1.60 (0.17), residues: 959 sheet: 0.13 (0.21), residues: 552 loop : -0.16 (0.16), residues: 1417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 372 time to evaluate : 3.769 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 49 residues processed: 437 average time/residue: 1.7967 time to fit residues: 968.6650 Evaluate side-chains 410 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 361 time to evaluate : 4.759 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 37 residues processed: 13 average time/residue: 0.6876 time to fit residues: 18.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 339 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 88 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN L 112 HIS O 103 ASN R 127 ASN a 43 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 53603 Z= 0.429 Angle : 0.689 12.173 78258 Z= 0.351 Chirality : 0.045 0.282 9728 Planarity : 0.006 0.063 5356 Dihedral : 15.070 179.039 18065 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.32 (0.15), residues: 2928 helix: 1.28 (0.17), residues: 960 sheet: -0.03 (0.21), residues: 542 loop : -0.35 (0.15), residues: 1426 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 366 time to evaluate : 3.945 Fit side-chains revert: symmetry clash outliers start: 105 outliers final: 69 residues processed: 430 average time/residue: 1.8859 time to fit residues: 992.1024 Evaluate side-chains 427 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 358 time to evaluate : 3.860 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 47 residues processed: 24 average time/residue: 0.8222 time to fit residues: 33.8802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 0.0040 chunk 358 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 398 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 209 optimal weight: 0.3980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN J 154 GLN O 83 GLN O 103 ASN R 127 ASN a 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 53603 Z= 0.137 Angle : 0.522 12.000 78258 Z= 0.270 Chirality : 0.035 0.259 9728 Planarity : 0.004 0.052 5356 Dihedral : 14.816 178.566 18065 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.65 (0.15), residues: 2928 helix: 1.64 (0.17), residues: 962 sheet: 0.13 (0.21), residues: 545 loop : -0.22 (0.16), residues: 1421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 370 time to evaluate : 4.204 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 55 residues processed: 424 average time/residue: 1.7960 time to fit residues: 939.4750 Evaluate side-chains 412 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 357 time to evaluate : 3.704 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 43 residues processed: 13 average time/residue: 0.7547 time to fit residues: 19.0086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 227 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 225 optimal weight: 0.0970 chunk 335 optimal weight: 8.9990 chunk 222 optimal weight: 0.0980 chunk 397 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN N 13 GLN O 83 GLN O 103 ASN R 127 ASN a 43 ASN j 158 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 53603 Z= 0.212 Angle : 0.543 12.042 78258 Z= 0.280 Chirality : 0.037 0.268 9728 Planarity : 0.004 0.054 5356 Dihedral : 14.710 178.207 18065 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.68 (0.15), residues: 2928 helix: 1.69 (0.17), residues: 960 sheet: 0.13 (0.21), residues: 550 loop : -0.21 (0.16), residues: 1418 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 359 time to evaluate : 5.024 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 54 residues processed: 417 average time/residue: 1.9083 time to fit residues: 979.7711 Evaluate side-chains 412 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 358 time to evaluate : 4.203 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 44 residues processed: 11 average time/residue: 0.6478 time to fit residues: 17.0205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 0.0070 chunk 158 optimal weight: 4.9990 chunk 237 optimal weight: 0.0050 chunk 119 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 overall best weight: 1.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN O 83 GLN O 103 ASN R 127 ASN a 43 ASN j 158 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 53603 Z= 0.207 Angle : 0.539 12.386 78258 Z= 0.278 Chirality : 0.037 0.265 9728 Planarity : 0.004 0.054 5356 Dihedral : 14.694 178.136 18065 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.69 (0.15), residues: 2928 helix: 1.68 (0.17), residues: 962 sheet: 0.14 (0.21), residues: 550 loop : -0.19 (0.16), residues: 1416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 355 time to evaluate : 3.880 Fit side-chains revert: symmetry clash outliers start: 75 outliers final: 58 residues processed: 415 average time/residue: 1.8725 time to fit residues: 955.4087 Evaluate side-chains 411 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 353 time to evaluate : 3.896 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 49 residues processed: 10 average time/residue: 0.5919 time to fit residues: 14.3818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 2.9990 chunk 380 optimal weight: 0.9980 chunk 347 optimal weight: 0.9980 chunk 370 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 290 optimal weight: 4.9990 chunk 113 optimal weight: 30.0000 chunk 334 optimal weight: 0.9990 chunk 349 optimal weight: 0.8980 chunk 368 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN O 83 GLN O 103 ASN a 43 ASN j 158 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 53603 Z= 0.144 Angle : 0.517 12.234 78258 Z= 0.268 Chirality : 0.035 0.265 9728 Planarity : 0.004 0.053 5356 Dihedral : 14.685 178.362 18065 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer Outliers : 2.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.76 (0.15), residues: 2928 helix: 1.76 (0.17), residues: 962 sheet: 0.16 (0.21), residues: 546 loop : -0.17 (0.16), residues: 1420 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 358 time to evaluate : 4.408 Fit side-chains revert: symmetry clash outliers start: 71 outliers final: 56 residues processed: 414 average time/residue: 1.8906 time to fit residues: 963.4741 Evaluate side-chains 413 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 357 time to evaluate : 3.903 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 49 residues processed: 8 average time/residue: 0.5005 time to fit residues: 11.8270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 7.9990 chunk 391 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 185 optimal weight: 0.0980 chunk 272 optimal weight: 0.8980 chunk 410 optimal weight: 1.9990 chunk 377 optimal weight: 0.0770 chunk 326 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN O 83 GLN O 103 ASN R 127 ASN a 43 ASN j 158 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 53603 Z= 0.125 Angle : 0.511 11.939 78258 Z= 0.265 Chirality : 0.034 0.262 9728 Planarity : 0.004 0.114 5356 Dihedral : 14.671 178.716 18065 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.79 (0.15), residues: 2928 helix: 1.77 (0.17), residues: 968 sheet: 0.19 (0.21), residues: 546 loop : -0.15 (0.16), residues: 1414 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5856 Ramachandran restraints generated. 2928 Oldfield, 0 Emsley, 2928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 358 time to evaluate : 3.690 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 52 residues processed: 411 average time/residue: 1.9047 time to fit residues: 966.1608 Evaluate side-chains 408 residues out of total 2564 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 356 time to evaluate : 4.202 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 49 residues processed: 4 average time/residue: 0.8487 time to fit residues: 10.0889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 4.9990 chunk 348 optimal weight: 0.2980 chunk 100 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 327 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 336 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** B 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 272 HIS ** H 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 167 GLN N 13 GLN O 83 GLN O 103 ASN a 43 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100419 restraints weight = 54534.370| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.04 r_work: 0.2984 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work: 0.2888 rms_B_bonded: 2.37 restraints_weight: 0.1250 r_work: 0.2814 rms_B_bonded: 3.40 restraints_weight: 0.0625 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 53603 Z= 0.407 Angle : 0.671 12.931 78258 Z= 0.342 Chirality : 0.044 0.284 9728 Planarity : 0.006 0.063 5356 Dihedral : 14.877 179.772 18065 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.44 (0.15), residues: 2928 helix: 1.44 (0.17), residues: 960 sheet: 0.08 (0.21), residues: 532 loop : -0.35 (0.15), residues: 1436 =============================================================================== Job complete usr+sys time: 13753.13 seconds wall clock time: 247 minutes 47.70 seconds (14867.70 seconds total)