Starting phenix.real_space_refine on Sun Sep 29 13:26:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/09_2024/6zoj_11320.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/09_2024/6zoj_11320.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/6zoj_11320/09_2024/6zoj_11320.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/09_2024/6zoj_11320.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/09_2024/6zoj_11320.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zoj_11320/09_2024/6zoj_11320.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1704 5.49 5 Mg 166 5.21 5 S 183 5.16 5 C 41026 2.51 5 N 13924 2.21 5 O 18777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 75783 Number of models: 1 Model: "" Number of chains: 45 Chain: "2" Number of atoms: 36367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1704, 36367 Classifications: {'RNA': 1704} Modifications used: {'rna2p_pur': 141, 'rna2p_pyr': 112, 'rna3p_pur': 756, 'rna3p_pyr': 695} Link IDs: {'rna2p': 253, 'rna3p': 1450} Chain breaks: 4 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: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1752 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 11, 'TRANS': 213} 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: "F" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1501 Classifications: {'peptide': 190} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 183} 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: "K" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 816 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 7, 'TRANS': 89} 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: "M" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} 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: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1016 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "R" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "S" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "T" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 95} 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: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 135} 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: "Z" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} 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: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "d" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 458 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} 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: "f" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 585 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "g" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} 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: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 159 Unusual residues: {' MG': 159} Classifications: {'undetermined': 159} Link IDs: {None: 158} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "S" 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: "T" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" 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 69429 SG CYS a 23 142.745 94.130 130.998 1.00 27.04 S ATOM 69450 SG CYS a 26 139.629 92.849 129.410 1.00 27.87 S ATOM 69833 SG CYS a 74 139.559 96.115 131.314 1.00 26.36 S ATOM 69852 SG CYS a 77 139.804 92.894 133.117 1.00 28.15 S ATOM 71350 SG CYS d 21 84.252 86.263 183.231 1.00 22.30 S ATOM 71374 SG CYS d 24 83.378 87.258 179.731 1.00 22.45 S ATOM 71495 SG CYS d 39 86.765 85.975 180.433 1.00 19.70 S ATOM 71521 SG CYS d 42 86.005 89.297 181.538 1.00 18.45 S ATOM 72456 SG CYS f 121 37.828 67.973 193.036 1.00 74.06 S ATOM 72492 SG CYS f 126 39.563 71.463 193.264 1.00 77.37 S ATOM 72610 SG CYS f 141 38.445 69.934 189.859 1.00 66.42 S ATOM 72629 SG CYS f 144 41.325 68.517 191.701 1.00 69.35 S Time building chain proxies: 31.54, per 1000 atoms: 0.42 Number of scatterers: 75783 At special positions: 0 Unit cell: (206.28, 231.12, 248.4, 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 3 29.99 S 183 16.00 P 1704 15.00 Mg 166 11.99 O 18777 8.00 N 13924 7.00 C 41026 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.17 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 201 " 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 77 " pdb="ZN ZN a 201 " - pdb=" SG CYS a 23 " pdb=" ZN d 201 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 42 " pdb="ZN ZN d 201 " - pdb=" SG CYS d 21 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 121 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 126 " Number of angles added : 18 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9106 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 58 sheets defined 38.2% alpha, 19.7% beta 466 base pairs and 870 stacking pairs defined. Time for finding SS restraints: 24.76 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: 3.685A pdb=" N GLN A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG A 85 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 138 removed outlier: 3.821A 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: 3.618A pdb=" N TYR A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 203 " --> pdb=" O ASP A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 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: 3.668A 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 85 removed outlier: 4.037A pdb=" N ILE C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 removed outlier: 3.613A pdb=" N ASP C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 removed outlier: 3.515A 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: 3.763A 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 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 269 through 276 Processing helix chain 'D' and resid 6 through 30 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 63 through 78 removed outlier: 3.645A pdb=" N ALA D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 removed outlier: 3.722A pdb=" N LEU D 96 " --> pdb=" O THR D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 93 through 96' Processing helix chain 'D' and resid 97 through 111 Processing helix chain 'D' and resid 114 through 130 removed outlier: 3.521A pdb=" N GLY D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 removed outlier: 4.213A pdb=" N TYR D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 14 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 37 through 41 removed outlier: 4.015A 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: 3.583A 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 'F' and resid 18 through 22 Processing helix chain 'F' and resid 33 through 38 removed outlier: 4.246A pdb=" N ASP F 37 " --> pdb=" O SER F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 67 through 76 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.597A pdb=" N ASN F 83 " --> pdb=" O GLY F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 105 removed outlier: 3.507A pdb=" N THR F 89 " --> pdb=" O LYS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 142 through 163 Processing helix chain 'F' and resid 168 through 183 Processing helix chain 'F' and resid 187 through 203 Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.629A pdb=" N LEU G 24 " --> pdb=" O ASP G 20 " (cutoff:3.500A) removed outlier: 4.438A 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 157 removed outlier: 4.085A pdb=" N VAL G 157 " --> pdb=" O ARG G 154 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 230 removed outlier: 3.887A pdb=" N LYS G 195 " --> pdb=" O ARG G 191 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN G 197 " --> pdb=" O ALA G 193 " (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: 3.614A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE H 75 " --> pdb=" O SER H 71 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 6.123A 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: 3.781A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 167 removed outlier: 3.741A 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 94 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 39 through 61 removed outlier: 4.178A pdb=" N VAL J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.600A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 92 removed outlier: 3.717A 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: 3.784A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.547A pdb=" N PHE J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 132 Processing helix chain 'J' and resid 150 through 155 removed outlier: 4.650A pdb=" N LYS J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 181 Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.592A pdb=" N ARG K 8 " --> pdb=" O PRO K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 55 Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'L' and resid 23 through 30 removed outlier: 3.546A pdb=" N THR L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 4.313A 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 'M' and resid 17 through 28 removed outlier: 4.143A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 44 Processing helix chain 'M' and resid 58 through 72 Processing helix chain 'M' and resid 81 through 90 Processing helix chain 'M' and resid 117 through 132 removed outlier: 3.562A pdb=" N VAL M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) 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: 4.052A 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: 4.239A pdb=" N SER N 147 " --> pdb=" O SER N 143 " (cutoff:3.500A) removed outlier: 4.597A 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: 4.333A 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 removed outlier: 3.506A pdb=" N LEU O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 122 removed outlier: 4.602A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 29 through 37 removed outlier: 3.814A pdb=" N GLN P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU P 36 " --> pdb=" O GLN P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 48 Processing helix chain 'P' and resid 50 through 66 Processing helix chain 'P' and resid 86 through 90 removed outlier: 3.576A pdb=" N VAL P 90 " --> pdb=" O PRO P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.633A pdb=" N ILE P 112 " --> pdb=" O PRO P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 116 through 120 removed outlier: 3.643A pdb=" N SER P 120 " --> pdb=" O GLY P 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 42 No H-bonds generated for 'chain 'Q' and resid 40 through 42' Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 59 removed outlier: 3.666A pdb=" N LEU Q 51 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 59 through 64 removed outlier: 3.899A pdb=" N PHE Q 63 " --> pdb=" O GLY Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 100 Processing helix chain 'Q' and resid 101 through 116 removed outlier: 3.708A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR Q 115 " --> pdb=" O ILE Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 120 Processing helix chain 'R' and resid 6 through 20 Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.532A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 Processing helix chain 'R' and resid 71 through 83 Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'S' and resid 25 through 30 removed outlier: 3.551A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 37 through 48 Processing helix chain 'S' and resid 55 through 59 removed outlier: 3.517A pdb=" N LEU S 59 " --> pdb=" O ALA S 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 73 Processing helix chain 'S' and resid 74 through 78 removed outlier: 3.760A pdb=" N LYS S 78 " --> pdb=" O ARG S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 99 through 118 removed outlier: 3.520A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 128 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 10 through 26 Processing helix chain 'T' and resid 31 through 36 removed outlier: 3.801A pdb=" N VAL T 34 " --> pdb=" O PRO T 31 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 67 removed outlier: 3.853A pdb=" N THR T 55 " --> pdb=" O ASN T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 79 Processing helix chain 'T' and resid 96 through 110 removed outlier: 3.637A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 124 through 145 Processing helix chain 'U' and resid 28 through 46 removed outlier: 3.641A pdb=" N LEU U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS U 46 " --> pdb=" O GLY U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 105 removed outlier: 3.623A pdb=" N VAL U 98 " --> pdb=" O PRO U 94 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE U 104 " --> pdb=" O GLN U 100 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER U 105 " --> pdb=" O ILE U 101 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 through 62 Processing helix chain 'V' and resid 64 through 76 Processing helix chain 'W' and resid 5 through 20 removed outlier: 3.734A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.771A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 removed outlier: 3.739A 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: 4.472A 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: 3.610A pdb=" N ASN X 92 " --> pdb=" O GLY X 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE X 94 " --> pdb=" O LEU X 91 " (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: 3.551A 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 'Z' and resid 51 through 61 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 69 through 78 Processing helix chain 'Z' and resid 80 through 95 Processing helix chain 'a' and resid 46 through 57 removed outlier: 3.598A pdb=" N ARG a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU a 55 " --> pdb=" O ARG a 51 " (cutoff:3.500A) removed outlier: 3.942A 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 removed outlier: 3.502A pdb=" N LYS b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 7 Processing helix chain 'd' and resid 15 through 19 Processing helix chain 'd' and resid 32 through 36 Processing helix chain 'd' and resid 40 through 51 removed outlier: 5.480A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 42 Processing helix chain 'f' and resid 102 through 104 No H-bonds generated for 'chain 'f' and resid 102 through 104' Processing helix chain 'g' and resid 276 through 280 removed outlier: 3.853A pdb=" N LYS g 280 " --> pdb=" O THR g 277 " (cutoff:3.500A) Processing helix chain 'j' and resid 152 through 161 Processing helix chain 'j' and resid 165 through 179 removed outlier: 3.563A pdb=" N ARG j 175 " --> pdb=" O ARG j 171 " (cutoff:3.500A) removed outlier: 3.510A 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: 6.995A 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: 6.792A pdb=" N VAL A 74 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE A 99 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 76 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR A 144 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ILE A 161 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.879A 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: 4.328A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 97 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LYS B 85 " --> pdb=" O HIS B 101 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N MET B 103 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS B 83 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 120 through 128 removed outlier: 3.715A pdb=" N LYS B 219 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL B 140 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B 213 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N PHE B 142 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N PHE B 211 " --> pdb=" O PHE B 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 103 through 115 removed outlier: 6.601A pdb=" N PHE C 127 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE C 109 " --> pdb=" O LYS C 125 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LYS C 125 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG C 123 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN C 113 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 6.203A 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 'D' and resid 34 through 41 removed outlier: 6.633A pdb=" N LEU D 51 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE D 49 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL D 39 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU D 47 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU D 85 " --> pdb=" O THR D 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 148 through 155 removed outlier: 3.741A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 209 through 210 removed outlier: 3.519A pdb=" N SER D 209 " --> pdb=" O ILE R 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 223 through 226 removed outlier: 6.435A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS g 153 " --> pdb=" O CYS g 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AB4, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.533A pdb=" N ILE E 102 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.730A 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: 6.566A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.917A pdb=" N ASN E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.246A 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: 6.435A pdb=" N MET E 182 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL E 227 " --> pdb=" O MET E 182 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 123 through 129 removed outlier: 25.467A pdb=" N ILE c 43 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 17.997A pdb=" N ARG F 136 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 13.439A pdb=" N ASN c 45 " --> pdb=" O ARG F 136 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ALA F 138 " --> pdb=" O ASN c 45 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LYS c 47 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP F 140 " --> pdb=" O LYS c 47 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N CYS c 27 " --> pdb=" O GLY c 19 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY c 19 " --> pdb=" O CYS c 27 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.401A pdb=" N LYS G 2 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU G 111 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ASN G 4 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE G 113 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER G 6 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LYS G 115 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL G 112 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE G 52 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL G 114 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL G 50 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AC1, first strand: chain 'G' and resid 160 through 162 Processing sheet with id=AC2, first strand: chain 'H' and resid 47 through 53 removed outlier: 6.857A pdb=" N LYS H 58 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL H 93 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 185 through 188 removed outlier: 8.368A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY H 141 " --> pdb=" O HIS H 157 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS H 142 " --> pdb=" O ASP W 54 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.274A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.249A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 62 through 67 removed outlier: 6.063A pdb=" N ARG I 77 " --> pdb=" O ASP I 105 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP I 105 " --> pdb=" O ARG I 77 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU I 103 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL I 81 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE I 101 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'K' and resid 20 through 23 Processing sheet with id=AC9, first strand: chain 'L' and resid 72 through 82 removed outlier: 16.852A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.842A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS L 81 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THR L 85 " --> pdb=" O LYS L 81 " (cutoff:3.500A) removed outlier: 10.079A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 31 through 33 removed outlier: 3.709A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 92 through 93 removed outlier: 3.507A pdb=" N LYS M 93 " --> pdb=" O LYS M 102 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS M 102 " --> pdb=" O LYS M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.860A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR O 57 " --> pdb=" O THR O 40 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR O 40 " --> pdb=" O THR O 57 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU O 93 " --> pdb=" O GLY O 127 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE O 129 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE O 95 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASP O 131 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU O 97 " --> pdb=" O ASP O 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 16 through 17 Processing sheet with id=AD5, first strand: chain 'P' and resid 76 through 78 Processing sheet with id=AD6, first strand: chain 'Q' and resid 9 through 15 removed outlier: 6.839A pdb=" N LYS Q 33 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL Q 72 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 96 through 98 Processing sheet with id=AD8, first strand: chain 'S' and resid 12 through 15 Processing sheet with id=AD9, first strand: chain 'T' and resid 81 through 85 removed outlier: 4.998A pdb=" N ASN T 85 " --> pdb=" O PRO T 89 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 113 through 115 Processing sheet with id=AE2, first strand: chain 'U' and resid 50 through 55 removed outlier: 5.792A pdb=" N LEU U 88 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG U 55 " --> pdb=" O LYS U 86 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS U 86 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 59 through 66 removed outlier: 8.958A pdb=" N ARG U 79 " --> pdb=" O LEU d 55 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU d 55 " --> pdb=" O ARG U 79 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 32 through 39 removed outlier: 4.997A pdb=" N GLN V 49 " --> pdb=" O GLU V 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 71 through 74 Processing sheet with id=AE6, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.568A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 128 through 129 removed outlier: 6.562A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 10.086A pdb=" N PHE X 120 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR X 82 " --> pdb=" O PHE X 120 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N VAL X 122 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N PHE X 84 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N LYS X 124 " --> pdb=" O PHE X 84 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 6 through 15 removed outlier: 4.293A pdb=" N PHE Y 12 " --> pdb=" O GLN Y 22 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN Y 22 " --> pdb=" O PHE Y 12 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR Y 14 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG Y 20 " --> pdb=" O THR Y 14 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS Y 68 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR Y 62 " --> pdb=" O LYS Y 68 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR Y 70 " --> pdb=" O PHE Y 60 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE Y 60 " --> pdb=" O THR Y 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 97 through 102 removed outlier: 6.882A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AF2, first strand: chain 'a' and resid 36 through 43 Processing sheet with id=AF3, first strand: chain 'b' and resid 43 through 47 Processing sheet with id=AF4, first strand: chain 'b' and resid 54 through 55 removed outlier: 6.709A pdb=" N VAL b 54 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 30 through 31 Processing sheet with id=AF6, first strand: chain 'f' and resid 106 through 108 Processing sheet with id=AF7, first strand: chain 'f' and resid 133 through 135 removed outlier: 3.515A pdb=" N ARG f 138 " --> pdb=" O HIS f 135 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 3 through 11 removed outlier: 5.441A pdb=" N MET g 5 " --> pdb=" O THR g 313 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR g 313 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEU g 7 " --> pdb=" O GLN g 311 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLN g 311 " --> pdb=" O LEU g 7 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY g 9 " --> pdb=" O VAL g 309 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 18 through 22 removed outlier: 3.555A pdb=" N GLN g 20 " --> pdb=" O ALA g 34 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE g 40 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA g 58 " --> pdb=" O ILE g 40 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET g 42 " --> pdb=" O GLN g 56 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 66 through 71 removed outlier: 3.554A pdb=" N ASP g 68 " --> pdb=" O GLY g 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU g 87 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG g 100 " --> pdb=" O LEU g 87 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU g 89 " --> pdb=" O THR g 98 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR g 96 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 108 through 113 removed outlier: 3.502A pdb=" N SER g 110 " --> pdb=" O GLY g 123 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.181A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 238 through 241 removed outlier: 3.761A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE g 256 " --> pdb=" O GLU g 269 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU g 269 " --> pdb=" O ILE g 256 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE g 258 " --> pdb=" O VAL g 267 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE g 265 " --> pdb=" O ASP g 260 " (cutoff:3.500A) 1626 hydrogen bonds defined for protein. 4563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1178 hydrogen bonds 1904 hydrogen bond angles 0 basepair planarities 466 basepair parallelities 870 stacking parallelities Total time for adding SS restraints: 66.67 Time building geometry restraints manager: 16.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15530 1.33 - 1.46: 27678 1.46 - 1.58: 33690 1.58 - 1.70: 3403 1.70 - 1.82: 279 Bond restraints: 80580 Sorted by residual: bond pdb=" N ALA F 131 " pdb=" CA ALA F 131 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.12e+00 bond pdb=" N LYS Q 17 " pdb=" CA LYS Q 17 " ideal model delta sigma weight residual 1.457 1.476 -0.019 1.17e-02 7.31e+03 2.58e+00 bond pdb=" N ALA S 100 " pdb=" CA ALA S 100 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.34e+00 bond pdb=" CA PRO a 97 " pdb=" C PRO a 97 " ideal model delta sigma weight residual 1.514 1.507 0.007 5.50e-03 3.31e+04 1.58e+00 bond pdb=" N GLU G 118 " pdb=" CA GLU G 118 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.43e+00 ... (remaining 80575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 115095 1.62 - 3.25: 1565 3.25 - 4.87: 219 4.87 - 6.49: 37 6.49 - 8.11: 9 Bond angle restraints: 116925 Sorted by residual: angle pdb=" N SER U 93 " pdb=" CA SER U 93 " pdb=" C SER U 93 " ideal model delta sigma weight residual 108.22 111.83 -3.61 9.00e-01 1.23e+00 1.61e+01 angle pdb=" N GLU X 53 " pdb=" CA GLU X 53 " pdb=" C GLU X 53 " ideal model delta sigma weight residual 107.88 113.35 -5.47 1.41e+00 5.03e-01 1.51e+01 angle pdb=" N VAL F 41 " pdb=" CA VAL F 41 " pdb=" C VAL F 41 " ideal model delta sigma weight residual 113.20 109.57 3.63 9.60e-01 1.09e+00 1.43e+01 angle pdb=" N SER O 139 " pdb=" CA SER O 139 " pdb=" C SER O 139 " ideal model delta sigma weight residual 108.34 113.00 -4.66 1.31e+00 5.83e-01 1.26e+01 angle pdb=" C VAL J 137 " pdb=" N ARG J 138 " pdb=" CA ARG J 138 " ideal model delta sigma weight residual 121.54 128.10 -6.56 1.91e+00 2.74e-01 1.18e+01 ... (remaining 116920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 46760 35.85 - 71.71: 4050 71.71 - 107.56: 522 107.56 - 143.41: 9 143.41 - 179.27: 20 Dihedral angle restraints: 51361 sinusoidal: 37242 harmonic: 14119 Sorted by residual: dihedral pdb=" O4' U 21551 " pdb=" C1' U 21551 " pdb=" N1 U 21551 " pdb=" C2 U 21551 " ideal model delta sinusoidal sigma weight residual -160.00 18.03 -178.03 1 1.50e+01 4.44e-03 8.53e+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 13.20 -173.20 1 1.50e+01 4.44e-03 8.50e+01 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 26.99 173.01 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 51358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 12596 0.048 - 0.096: 1423 0.096 - 0.145: 398 0.145 - 0.193: 19 0.193 - 0.241: 6 Chirality restraints: 14442 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 2.23 0.24 2.00e-01 2.50e+01 1.45e+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 2.25 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1' U 21445 " pdb=" O4' U 21445 " pdb=" C2' U 21445 " pdb=" N1 U 21445 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 14439 not shown) Planarity restraints: 8511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 21240 " -0.037 2.00e-02 2.50e+03 1.66e-02 7.56e+00 pdb=" N9 A 21240 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A 21240 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 21240 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 21240 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 21240 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 21240 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A 21240 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A 21240 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 21240 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 21240 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21311 " -0.032 2.00e-02 2.50e+03 1.68e-02 6.35e+00 pdb=" N1 C 21311 " 0.036 2.00e-02 2.50e+03 pdb=" C2 C 21311 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C 21311 " 0.003 2.00e-02 2.50e+03 pdb=" N3 C 21311 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C 21311 " -0.004 2.00e-02 2.50e+03 pdb=" N4 C 21311 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C 21311 " 0.002 2.00e-02 2.50e+03 pdb=" C6 C 21311 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21606 " -0.032 2.00e-02 2.50e+03 1.36e-02 5.59e+00 pdb=" N9 G 21606 " 0.032 2.00e-02 2.50e+03 pdb=" C8 G 21606 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 21606 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 21606 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 21606 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G 21606 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G 21606 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 21606 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 21606 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 21606 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G 21606 " 0.005 2.00e-02 2.50e+03 ... (remaining 8508 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.34: 129 2.34 - 2.98: 33868 2.98 - 3.62: 113909 3.62 - 4.26: 208130 4.26 - 4.90: 297892 Nonbonded interactions: 653928 Sorted by model distance: nonbonded pdb="MG MG 22012 " pdb="MG MG 22043 " model vdw 1.694 1.300 nonbonded pdb=" OP1 G 21837 " pdb="MG MG 22090 " model vdw 1.976 2.170 nonbonded pdb=" OP2 A 2 46 " pdb="MG MG 22148 " model vdw 2.007 2.170 nonbonded pdb=" OP2 G 21603 " pdb="MG MG 22031 " model vdw 2.013 2.170 nonbonded pdb=" O6 G 21517 " pdb="MG MG 22001 " model vdw 2.025 2.170 ... (remaining 653923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.090 Extract box with map and model: 2.330 Check model and map are aligned: 0.450 Set scattering table: 0.540 Process input model: 193.440 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 219.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 0.037 80580 Z= 0.143 Angle : 0.511 8.114 116925 Z= 0.287 Chirality : 0.034 0.241 14442 Planarity : 0.003 0.046 8511 Dihedral : 21.179 179.267 42252 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.39 % Allowed : 3.75 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4844 helix: 1.63 (0.13), residues: 1614 sheet: 0.46 (0.17), residues: 935 loop : -0.22 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 64 HIS 0.003 0.001 HIS R 29 PHE 0.015 0.001 PHE D 79 TYR 0.013 0.001 TYR F 188 ARG 0.004 0.000 ARG a 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 849 time to evaluate : 4.347 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: B 95 ASN cc_start: 0.8079 (m-40) cc_final: 0.7677 (m-40) REVERT: B 229 MET cc_start: 0.8022 (mmm) cc_final: 0.7652 (mpm) REVERT: D 120 TYR cc_start: 0.7792 (m-80) cc_final: 0.7365 (m-80) REVERT: D 206 ASP cc_start: 0.7886 (p0) cc_final: 0.7642 (p0) REVERT: E 115 THR cc_start: 0.8751 (m) cc_final: 0.8536 (p) REVERT: G 156 TYR cc_start: 0.8421 (m-80) cc_final: 0.8140 (m-80) REVERT: H 32 MET cc_start: 0.6251 (mmt) cc_final: 0.5857 (ptt) REVERT: H 81 ARG cc_start: 0.6843 (ttp-170) cc_final: 0.6136 (tpm170) REVERT: I 99 ASN cc_start: 0.8870 (t0) cc_final: 0.8443 (t160) REVERT: K 1 MET cc_start: 0.8678 (ttt) cc_final: 0.8296 (ttt) REVERT: K 77 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7203 (mm-40) REVERT: O 83 GLN cc_start: 0.8269 (tp40) cc_final: 0.8026 (tp-100) REVERT: R 35 CYS cc_start: 0.7314 (m) cc_final: 0.7113 (m) REVERT: R 126 MET cc_start: 0.5127 (ptp) cc_final: 0.4806 (ptp) REVERT: S 89 ASP cc_start: 0.7656 (t0) cc_final: 0.7420 (t0) REVERT: S 92 ASP cc_start: 0.7693 (p0) cc_final: 0.7476 (OUTLIER) REVERT: U 68 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8572 (t) REVERT: V 50 PHE cc_start: 0.8260 (p90) cc_final: 0.7962 (p90) REVERT: b 79 PHE cc_start: 0.8312 (p90) cc_final: 0.8078 (p90) REVERT: e 40 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7638 (ttp80) REVERT: g 165 ILE cc_start: 0.7871 (OUTLIER) cc_final: 0.7316 (mt) REVERT: g 192 THR cc_start: 0.7599 (m) cc_final: 0.7352 (p) outliers start: 59 outliers final: 21 residues processed: 890 average time/residue: 1.8360 time to fit residues: 2144.7871 Evaluate side-chains 615 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 593 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 309 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 548 optimal weight: 5.9990 chunk 491 optimal weight: 0.8980 chunk 272 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 331 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 508 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 378 optimal weight: 7.9990 chunk 589 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 B 177 GLN C 178 HIS D 145 GLN E 161 GLN E 209 HIS F 36 GLN F 83 ASN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 111 GLN I 168 GLN J 27 GLN O 103 ASN P 24 GLN P 46 ASN P 103 ASN Q 8 GLN Q 114 GLN R 62 GLN T 137 GLN U 81 GLN V 21 ASN Z 89 GLN a 43 ASN ** c 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 226 HIS g 296 GLN j 160 ASN j 165 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 80580 Z= 0.339 Angle : 0.622 10.450 116925 Z= 0.320 Chirality : 0.041 0.264 14442 Planarity : 0.005 0.056 8511 Dihedral : 22.893 179.943 32111 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.45 % Allowed : 11.00 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % 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: 0.60 (0.12), residues: 4844 helix: 1.55 (0.13), residues: 1643 sheet: 0.37 (0.17), residues: 936 loop : -0.39 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 132 HIS 0.007 0.001 HIS H 126 PHE 0.017 0.002 PHE O 41 TYR 0.017 0.002 TYR I 27 ARG 0.008 0.001 ARG T 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 610 time to evaluate : 4.498 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: B 27 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8354 (pmtt) REVERT: B 229 MET cc_start: 0.8011 (mmm) cc_final: 0.7568 (mpm) REVERT: D 120 TYR cc_start: 0.7858 (m-80) cc_final: 0.7460 (m-80) REVERT: D 189 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8197 (ttt) REVERT: D 206 ASP cc_start: 0.8027 (p0) cc_final: 0.7790 (p0) REVERT: G 168 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5905 (pttt) REVERT: G 197 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7353 (mp-120) REVERT: H 81 ARG cc_start: 0.6725 (ttp-170) cc_final: 0.6105 (tpm170) REVERT: I 99 ASN cc_start: 0.8857 (t0) cc_final: 0.8388 (t160) REVERT: I 117 TYR cc_start: 0.8226 (m-80) cc_final: 0.7967 (m-80) REVERT: J 34 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: K 1 MET cc_start: 0.8755 (ttt) cc_final: 0.8367 (ttt) REVERT: K 77 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7405 (mm-40) REVERT: L 8 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7192 (mtt180) REVERT: N 72 LEU cc_start: 0.8243 (tp) cc_final: 0.7964 (mt) REVERT: O 83 GLN cc_start: 0.8291 (tp40) cc_final: 0.8084 (tp-100) REVERT: R 126 MET cc_start: 0.5473 (ptp) cc_final: 0.5101 (ptp) REVERT: S 8 LYS cc_start: 0.8237 (pmtt) cc_final: 0.7821 (pttp) REVERT: S 14 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7379 (tmt-80) REVERT: S 89 ASP cc_start: 0.7776 (t0) cc_final: 0.7519 (t0) REVERT: V 21 ASN cc_start: 0.8674 (t0) cc_final: 0.8447 (t0) REVERT: V 50 PHE cc_start: 0.8322 (p90) cc_final: 0.8044 (p90) REVERT: b 80 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7120 (ttt180) REVERT: e 40 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.7698 (ttp80) REVERT: f 148 TYR cc_start: 0.7394 (m-80) cc_final: 0.7194 (m-80) REVERT: g 265 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7629 (pp) outliers start: 146 outliers final: 68 residues processed: 690 average time/residue: 1.7914 time to fit residues: 1634.6641 Evaluate side-chains 637 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 560 time to evaluate : 6.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain B residue 27 LYS Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain E residue 196 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 168 LYS Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 92 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 60 LYS Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 80 ARG Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 149 CYS Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 265 ILE Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 490 optimal weight: 5.9990 chunk 401 optimal weight: 0.6980 chunk 162 optimal weight: 10.0000 chunk 590 optimal weight: 4.9990 chunk 637 optimal weight: 0.9990 chunk 525 optimal weight: 0.8980 chunk 585 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 473 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 177 GLN C 113 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN I 168 GLN J 27 GLN K 39 ASN L 112 HIS O 103 ASN P 24 GLN Q 114 GLN R 62 GLN T 137 GLN T 142 ASN U 81 GLN V 47 ASN W 91 ASN Z 89 GLN a 43 ASN j 158 GLN j 160 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 80580 Z= 0.235 Angle : 0.564 10.480 116925 Z= 0.293 Chirality : 0.038 0.261 14442 Planarity : 0.004 0.046 8511 Dihedral : 22.839 179.847 32106 Min Nonbonded Distance : 1.247 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.16 % Allowed : 12.58 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4844 helix: 1.66 (0.13), residues: 1644 sheet: 0.35 (0.17), residues: 934 loop : -0.40 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 132 HIS 0.005 0.001 HIS H 126 PHE 0.016 0.002 PHE e 42 TYR 0.018 0.001 TYR f 148 ARG 0.008 0.001 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 601 time to evaluate : 5.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 229 MET cc_start: 0.8054 (mmm) cc_final: 0.7636 (mpm) REVERT: D 120 TYR cc_start: 0.7843 (m-80) cc_final: 0.7549 (m-80) REVERT: D 206 ASP cc_start: 0.8060 (p0) cc_final: 0.7803 (p0) REVERT: D 227 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5447 (ptmm) REVERT: G 22 ARG cc_start: 0.7447 (mpp80) cc_final: 0.7180 (mtm-85) REVERT: G 35 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: G 148 SER cc_start: 0.7343 (p) cc_final: 0.6892 (t) REVERT: G 197 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7408 (mp-120) REVERT: H 32 MET cc_start: 0.6550 (mmt) cc_final: 0.6076 (ptt) REVERT: H 81 ARG cc_start: 0.6686 (ttp-170) cc_final: 0.6086 (tpm170) REVERT: I 99 ASN cc_start: 0.8827 (t0) cc_final: 0.8362 (t160) REVERT: J 34 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: K 1 MET cc_start: 0.8747 (ttt) cc_final: 0.8309 (ttt) REVERT: K 77 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7217 (mm-40) REVERT: O 83 GLN cc_start: 0.8326 (tp40) cc_final: 0.8067 (tp-100) REVERT: O 129 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8466 (mm) REVERT: P 136 THR cc_start: 0.6049 (m) cc_final: 0.5794 (p) REVERT: S 8 LYS cc_start: 0.8252 (pmtt) cc_final: 0.7724 (pttp) REVERT: S 14 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7366 (tmt-80) REVERT: S 89 ASP cc_start: 0.7814 (t0) cc_final: 0.7606 (t0) REVERT: U 68 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8585 (t) REVERT: V 21 ASN cc_start: 0.8708 (t0) cc_final: 0.8429 (t0) REVERT: V 50 PHE cc_start: 0.8340 (p90) cc_final: 0.8033 (p90) REVERT: c 35 MET cc_start: 0.8239 (mmm) cc_final: 0.7779 (mtm) REVERT: j 160 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7344 (m-40) outliers start: 134 outliers final: 73 residues processed: 677 average time/residue: 1.6688 time to fit residues: 1487.7883 Evaluate side-chains 650 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 569 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain N residue 149 LEU Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 149 CYS Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain j residue 160 ASN Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 583 optimal weight: 0.4980 chunk 443 optimal weight: 0.0170 chunk 306 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 281 optimal weight: 0.7980 chunk 396 optimal weight: 4.9990 chunk 592 optimal weight: 4.9990 chunk 627 optimal weight: 6.9990 chunk 309 optimal weight: 1.9990 chunk 561 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 177 GLN D 179 GLN E 214 ASN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 186 ASN I 7 ASN J 27 GLN P 46 ASN Q 114 GLN R 62 GLN T 142 ASN V 47 ASN Z 89 GLN a 43 ASN b 29 ASN b 49 HIS j 158 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 80580 Z= 0.168 Angle : 0.531 10.945 116925 Z= 0.276 Chirality : 0.036 0.255 14442 Planarity : 0.004 0.046 8511 Dihedral : 22.791 179.757 32105 Min Nonbonded Distance : 1.190 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.76 % Allowed : 13.83 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.78 (0.12), residues: 4844 helix: 1.77 (0.13), residues: 1639 sheet: 0.43 (0.17), residues: 925 loop : -0.32 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 132 HIS 0.005 0.001 HIS H 126 PHE 0.018 0.001 PHE b 79 TYR 0.014 0.001 TYR g 246 ARG 0.007 0.000 ARG e 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 599 time to evaluate : 4.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8079 (mtp) cc_final: 0.7840 (mtm) REVERT: B 229 MET cc_start: 0.8026 (mmm) cc_final: 0.7628 (mpm) REVERT: D 120 TYR cc_start: 0.7790 (m-80) cc_final: 0.7519 (m-80) REVERT: D 206 ASP cc_start: 0.8054 (p0) cc_final: 0.7808 (p0) REVERT: E 117 GLU cc_start: 0.7736 (mp0) cc_final: 0.7455 (mp0) REVERT: G 35 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7699 (mm-30) REVERT: G 148 SER cc_start: 0.7351 (p) cc_final: 0.6702 (t) REVERT: G 197 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7391 (mp-120) REVERT: H 32 MET cc_start: 0.6500 (mmt) cc_final: 0.5930 (ptp) REVERT: H 81 ARG cc_start: 0.6690 (ttp-170) cc_final: 0.6116 (tpm170) REVERT: I 99 ASN cc_start: 0.8804 (t0) cc_final: 0.8336 (t160) REVERT: J 27 GLN cc_start: 0.7993 (mt0) cc_final: 0.7663 (mt0) REVERT: J 34 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: K 1 MET cc_start: 0.8749 (ttt) cc_final: 0.8303 (ttt) REVERT: K 77 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7358 (mm-40) REVERT: O 83 GLN cc_start: 0.8399 (tp40) cc_final: 0.8144 (tp-100) REVERT: O 129 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8444 (mm) REVERT: P 66 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7365 (mt-10) REVERT: P 136 THR cc_start: 0.6072 (m) cc_final: 0.5832 (p) REVERT: S 8 LYS cc_start: 0.8238 (pmtt) cc_final: 0.7708 (pttp) REVERT: S 14 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7473 (tmt-80) REVERT: U 68 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8544 (t) REVERT: V 21 ASN cc_start: 0.8653 (t0) cc_final: 0.8336 (t0) REVERT: V 50 PHE cc_start: 0.8328 (p90) cc_final: 0.8034 (p90) REVERT: Z 97 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7934 (pt) REVERT: b 16 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8609 (tmtp) REVERT: c 35 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7798 (mtm) outliers start: 117 outliers final: 71 residues processed: 664 average time/residue: 1.6544 time to fit residues: 1445.8399 Evaluate side-chains 649 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 569 time to evaluate : 4.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 64 TRP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 35 MET Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 149 CYS Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 522 optimal weight: 4.9990 chunk 356 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 467 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 chunk 535 optimal weight: 0.9980 chunk 433 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 320 optimal weight: 0.9980 chunk 563 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 177 GLN D 179 GLN F 36 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN P 24 GLN P 46 ASN Q 97 GLN Q 114 GLN R 62 GLN T 117 GLN T 142 ASN V 47 ASN Z 89 GLN a 43 ASN b 29 ASN ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 ASN j 158 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 80580 Z= 0.181 Angle : 0.530 11.052 116925 Z= 0.274 Chirality : 0.036 0.252 14442 Planarity : 0.004 0.045 8511 Dihedral : 22.737 179.992 32105 Min Nonbonded Distance : 1.156 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.11 % Allowed : 14.04 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.85 (0.12), residues: 4844 helix: 1.84 (0.13), residues: 1636 sheet: 0.43 (0.17), residues: 935 loop : -0.28 (0.12), residues: 2273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 132 HIS 0.004 0.001 HIS Y 89 PHE 0.019 0.001 PHE b 79 TYR 0.015 0.001 TYR Y 97 ARG 0.009 0.000 ARG I 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 590 time to evaluate : 4.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8098 (mtp) cc_final: 0.7883 (mtm) REVERT: B 229 MET cc_start: 0.8041 (mmm) cc_final: 0.7719 (mpm) REVERT: C 227 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7617 (ttm170) REVERT: D 120 TYR cc_start: 0.7756 (m-80) cc_final: 0.7553 (m-80) REVERT: D 206 ASP cc_start: 0.8031 (p0) cc_final: 0.7767 (p0) REVERT: D 227 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5319 (ptmm) REVERT: E 117 GLU cc_start: 0.7737 (mp0) cc_final: 0.7535 (mp0) REVERT: G 22 ARG cc_start: 0.7528 (mpp80) cc_final: 0.7262 (mtm-85) REVERT: G 35 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7739 (mm-30) REVERT: G 148 SER cc_start: 0.7297 (p) cc_final: 0.6621 (t) REVERT: H 32 MET cc_start: 0.6478 (mmt) cc_final: 0.5963 (ptp) REVERT: H 81 ARG cc_start: 0.6709 (ttp-170) cc_final: 0.6123 (tpm170) REVERT: I 99 ASN cc_start: 0.8787 (t0) cc_final: 0.8308 (t160) REVERT: J 34 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: K 1 MET cc_start: 0.8762 (ttt) cc_final: 0.8314 (ttt) REVERT: K 77 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7378 (mm-40) REVERT: L 8 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7211 (mtt180) REVERT: O 83 GLN cc_start: 0.8397 (tp40) cc_final: 0.8172 (tp-100) REVERT: O 129 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8474 (mm) REVERT: P 136 THR cc_start: 0.6054 (m) cc_final: 0.5813 (p) REVERT: S 8 LYS cc_start: 0.8263 (pmtt) cc_final: 0.7690 (pttp) REVERT: S 14 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7473 (tmt-80) REVERT: U 68 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8545 (t) REVERT: V 21 ASN cc_start: 0.8665 (t0) cc_final: 0.8318 (t0) REVERT: V 50 PHE cc_start: 0.8333 (p90) cc_final: 0.8019 (p90) REVERT: Z 97 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7882 (pt) REVERT: b 3 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8507 (mp) REVERT: b 16 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8635 (tmtp) REVERT: c 35 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7833 (mtm) outliers start: 132 outliers final: 75 residues processed: 667 average time/residue: 1.6287 time to fit residues: 1426.0917 Evaluate side-chains 651 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 564 time to evaluate : 4.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 130 THR Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 35 MET Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 149 CYS Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 211 optimal weight: 0.6980 chunk 564 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 368 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 627 optimal weight: 0.9980 chunk 521 optimal weight: 2.9990 chunk 290 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 329 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 177 GLN D 179 GLN F 36 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN P 46 ASN Q 114 GLN T 117 GLN T 142 ASN U 81 GLN V 47 ASN W 70 ASN Z 89 GLN a 43 ASN b 29 ASN c 29 GLN j 158 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 80580 Z= 0.182 Angle : 0.532 11.523 116925 Z= 0.275 Chirality : 0.036 0.249 14442 Planarity : 0.004 0.044 8511 Dihedral : 22.714 179.986 32103 Min Nonbonded Distance : 1.159 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.97 % Allowed : 14.70 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.88 (0.12), residues: 4844 helix: 1.87 (0.13), residues: 1644 sheet: 0.44 (0.17), residues: 928 loop : -0.26 (0.13), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 132 HIS 0.004 0.001 HIS Y 89 PHE 0.022 0.001 PHE b 79 TYR 0.014 0.001 TYR M 61 ARG 0.008 0.000 ARG V 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 594 time to evaluate : 4.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 113 MET cc_start: 0.8115 (mtp) cc_final: 0.7903 (mtm) REVERT: B 229 MET cc_start: 0.8035 (mmm) cc_final: 0.7734 (mpm) REVERT: C 227 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7616 (ttm170) REVERT: D 206 ASP cc_start: 0.8030 (p0) cc_final: 0.7771 (p0) REVERT: D 227 LYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5299 (ptmm) REVERT: E 197 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8436 (p0) REVERT: G 22 ARG cc_start: 0.7460 (mpp80) cc_final: 0.7256 (mtm-85) REVERT: G 35 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: G 148 SER cc_start: 0.7497 (p) cc_final: 0.6763 (t) REVERT: H 32 MET cc_start: 0.6469 (mmt) cc_final: 0.5939 (ptm) REVERT: H 81 ARG cc_start: 0.6667 (ttp-170) cc_final: 0.6073 (tpm170) REVERT: I 99 ASN cc_start: 0.8796 (t0) cc_final: 0.8320 (t160) REVERT: J 34 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: K 77 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7373 (mm-40) REVERT: L 8 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7213 (mtt180) REVERT: O 129 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8464 (mm) REVERT: P 136 THR cc_start: 0.6068 (m) cc_final: 0.5837 (p) REVERT: S 8 LYS cc_start: 0.8238 (pmtt) cc_final: 0.7675 (pttp) REVERT: S 14 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7476 (tmt-80) REVERT: U 68 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (t) REVERT: V 21 ASN cc_start: 0.8643 (t0) cc_final: 0.8339 (t0) REVERT: V 50 PHE cc_start: 0.8362 (p90) cc_final: 0.8038 (p90) REVERT: Z 97 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7857 (pt) REVERT: b 3 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8513 (mp) REVERT: b 16 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8585 (tmtp) REVERT: c 35 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7786 (mtm) outliers start: 126 outliers final: 86 residues processed: 671 average time/residue: 1.6453 time to fit residues: 1457.2648 Evaluate side-chains 667 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 568 time to evaluate : 4.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 160 SER Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 71 MET Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain T residue 85 ASN Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 66 THR Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 35 MET Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 149 CYS Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 225 LYS Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 605 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 357 optimal weight: 2.9990 chunk 458 optimal weight: 1.9990 chunk 355 optimal weight: 9.9990 chunk 528 optimal weight: 2.9990 chunk 350 optimal weight: 1.9990 chunk 625 optimal weight: 9.9990 chunk 391 optimal weight: 7.9990 chunk 381 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS D 179 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 7 ASN N 69 ASN O 103 ASN P 24 GLN P 104 GLN Q 114 GLN T 117 GLN T 142 ASN U 81 GLN V 47 ASN W 90 GLN Z 89 GLN a 43 ASN b 29 ASN c 29 GLN j 158 GLN j 160 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 80580 Z= 0.284 Angle : 0.590 12.130 116925 Z= 0.303 Chirality : 0.039 0.262 14442 Planarity : 0.005 0.046 8511 Dihedral : 22.730 179.827 32103 Min Nonbonded Distance : 1.117 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.49 % Allowed : 14.94 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.75 (0.12), residues: 4844 helix: 1.78 (0.13), residues: 1630 sheet: 0.30 (0.17), residues: 943 loop : -0.32 (0.12), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP g 132 HIS 0.005 0.001 HIS Y 89 PHE 0.024 0.002 PHE b 79 TYR 0.016 0.002 TYR g 246 ARG 0.010 0.001 ARG e 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 577 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8437 (tmtp) REVERT: B 113 MET cc_start: 0.8137 (mtp) cc_final: 0.7928 (mtm) REVERT: B 147 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7435 (t0) REVERT: B 170 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7526 (pt0) REVERT: B 229 MET cc_start: 0.8058 (mmm) cc_final: 0.7713 (mpm) REVERT: D 120 TYR cc_start: 0.7669 (m-80) cc_final: 0.7469 (m-80) REVERT: D 206 ASP cc_start: 0.8082 (p0) cc_final: 0.7827 (p0) REVERT: D 227 LYS cc_start: 0.5519 (OUTLIER) cc_final: 0.5277 (ptmm) REVERT: G 148 SER cc_start: 0.7367 (p) cc_final: 0.6685 (t) REVERT: H 32 MET cc_start: 0.6457 (mmt) cc_final: 0.5991 (ptp) REVERT: H 81 ARG cc_start: 0.6712 (ttp-170) cc_final: 0.6075 (tpm170) REVERT: I 99 ASN cc_start: 0.8817 (t0) cc_final: 0.8315 (t160) REVERT: J 27 GLN cc_start: 0.8018 (mt0) cc_final: 0.7665 (mt0) REVERT: J 34 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: K 77 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7482 (mm-40) REVERT: L 8 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7201 (mtt180) REVERT: O 129 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8478 (mm) REVERT: P 136 THR cc_start: 0.6096 (m) cc_final: 0.5850 (p) REVERT: R 103 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8099 (tttp) REVERT: S 8 LYS cc_start: 0.8213 (pmtt) cc_final: 0.7638 (pttp) REVERT: S 14 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7471 (tmt-80) REVERT: V 21 ASN cc_start: 0.8579 (t0) cc_final: 0.8244 (t0) REVERT: V 50 PHE cc_start: 0.8330 (p90) cc_final: 0.8028 (p90) REVERT: b 16 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8599 (tmtp) REVERT: c 35 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7883 (mtm) outliers start: 148 outliers final: 89 residues processed: 670 average time/residue: 1.6536 time to fit residues: 1463.3435 Evaluate side-chains 662 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 563 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 55 ILE Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 35 MET Chi-restraints excluded: chain d residue 53 ILE Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 149 CYS Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 386 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 373 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 397 optimal weight: 2.9990 chunk 426 optimal weight: 0.9980 chunk 309 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 491 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 177 GLN D 179 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN N 69 ASN P 104 GLN Q 114 GLN R 62 GLN T 117 GLN T 142 ASN U 81 GLN V 47 ASN W 15 ASN Z 89 GLN a 43 ASN b 29 ASN c 29 GLN j 158 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 80580 Z= 0.229 Angle : 0.571 12.847 116925 Z= 0.294 Chirality : 0.038 0.259 14442 Planarity : 0.004 0.081 8511 Dihedral : 22.747 179.989 32102 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.88 % Allowed : 15.86 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.75 (0.12), residues: 4844 helix: 1.79 (0.13), residues: 1629 sheet: 0.32 (0.17), residues: 933 loop : -0.33 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 132 HIS 0.005 0.001 HIS R 56 PHE 0.024 0.001 PHE b 79 TYR 0.027 0.001 TYR f 148 ARG 0.010 0.000 ARG V 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 577 time to evaluate : 4.599 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: A 40 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8441 (tmtp) REVERT: B 113 MET cc_start: 0.8133 (mtp) cc_final: 0.7919 (mtm) REVERT: B 147 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.7429 (t0) REVERT: B 170 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: D 120 TYR cc_start: 0.7710 (m-80) cc_final: 0.7485 (m-80) REVERT: D 206 ASP cc_start: 0.8097 (p0) cc_final: 0.7817 (p0) REVERT: G 148 SER cc_start: 0.7359 (p) cc_final: 0.6677 (t) REVERT: H 81 ARG cc_start: 0.6709 (ttp-170) cc_final: 0.6073 (tpm170) REVERT: I 99 ASN cc_start: 0.8784 (t0) cc_final: 0.8299 (t160) REVERT: J 34 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7191 (tm-30) REVERT: K 77 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7501 (mm110) REVERT: L 8 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7199 (mtt180) REVERT: M 43 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6470 (t0) REVERT: O 129 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8494 (mm) REVERT: P 136 THR cc_start: 0.6105 (m) cc_final: 0.5871 (p) REVERT: R 103 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8113 (tttp) REVERT: S 8 LYS cc_start: 0.8216 (pmtt) cc_final: 0.7633 (pttp) REVERT: S 14 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7480 (tmt-80) REVERT: V 21 ASN cc_start: 0.8571 (t0) cc_final: 0.8237 (t0) REVERT: V 50 PHE cc_start: 0.8340 (p90) cc_final: 0.8028 (p90) REVERT: b 16 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8611 (tmtp) REVERT: c 35 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7843 (mtm) REVERT: g 269 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5859 (tm-30) REVERT: h 13 LEU cc_start: 0.8575 (tt) cc_final: 0.8221 (tp) outliers start: 122 outliers final: 90 residues processed: 654 average time/residue: 1.6880 time to fit residues: 1455.0624 Evaluate side-chains 671 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 570 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 35 MET Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 149 CYS Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 269 GLU Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 569 optimal weight: 4.9990 chunk 599 optimal weight: 1.9990 chunk 546 optimal weight: 0.7980 chunk 582 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 253 optimal weight: 4.9990 chunk 457 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 chunk 526 optimal weight: 7.9990 chunk 551 optimal weight: 2.9990 chunk 580 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS B 177 GLN D 179 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 7 ASN I 138 ASN N 69 ASN P 46 ASN P 104 GLN R 62 GLN T 117 GLN T 142 ASN U 81 GLN V 47 ASN W 15 ASN W 91 ASN Z 89 GLN a 43 ASN b 29 ASN c 29 GLN j 158 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 80580 Z= 0.261 Angle : 0.585 13.806 116925 Z= 0.301 Chirality : 0.039 0.262 14442 Planarity : 0.005 0.075 8511 Dihedral : 22.733 179.806 32102 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.02 % Allowed : 15.93 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % 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: 0.71 (0.12), residues: 4844 helix: 1.75 (0.13), residues: 1626 sheet: 0.32 (0.17), residues: 923 loop : -0.34 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 132 HIS 0.005 0.001 HIS Y 89 PHE 0.024 0.002 PHE b 79 TYR 0.017 0.001 TYR g 246 ARG 0.010 0.000 ARG V 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 580 time to evaluate : 4.404 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: A 36 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8244 (pt0) REVERT: A 40 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8435 (tmtp) REVERT: B 113 MET cc_start: 0.8143 (mtp) cc_final: 0.7928 (mtm) REVERT: B 147 ASN cc_start: 0.7747 (OUTLIER) cc_final: 0.7441 (t0) REVERT: B 170 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: B 229 MET cc_start: 0.8219 (mmt) cc_final: 0.7841 (mpm) REVERT: D 120 TYR cc_start: 0.7761 (m-80) cc_final: 0.7482 (m-80) REVERT: D 206 ASP cc_start: 0.8114 (p0) cc_final: 0.7845 (p0) REVERT: G 148 SER cc_start: 0.7380 (p) cc_final: 0.6693 (t) REVERT: H 81 ARG cc_start: 0.6721 (ttp-170) cc_final: 0.6083 (tpm170) REVERT: I 99 ASN cc_start: 0.8788 (t0) cc_final: 0.8301 (t160) REVERT: J 34 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: K 77 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7499 (mm110) REVERT: L 8 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7200 (mtt180) REVERT: M 43 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.6497 (t0) REVERT: O 129 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8485 (mm) REVERT: P 136 THR cc_start: 0.6214 (m) cc_final: 0.5985 (p) REVERT: R 103 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8092 (tttp) REVERT: S 8 LYS cc_start: 0.8210 (pmtt) cc_final: 0.7676 (pttp) REVERT: S 14 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7496 (tmt-80) REVERT: V 21 ASN cc_start: 0.8570 (t0) cc_final: 0.8233 (t0) REVERT: V 50 PHE cc_start: 0.8352 (p90) cc_final: 0.8077 (p90) REVERT: b 16 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8613 (tmtp) REVERT: c 35 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: c 52 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: g 91 ASP cc_start: 0.7963 (t70) cc_final: 0.7706 (p0) REVERT: g 269 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5932 (tm-30) REVERT: h 13 LEU cc_start: 0.8558 (tt) cc_final: 0.8193 (tp) outliers start: 128 outliers final: 90 residues processed: 659 average time/residue: 1.6291 time to fit residues: 1416.7026 Evaluate side-chains 665 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 562 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 209 SER Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain L residue 8 ARG Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 118 ARG Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain M residue 43 ASP Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 144 SER Chi-restraints excluded: chain O residue 48 SER Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 12 ILE Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain c residue 35 MET Chi-restraints excluded: chain c residue 52 GLU Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain f residue 149 CYS Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 269 GLU Chi-restraints excluded: chain g residue 274 VAL Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 382 optimal weight: 0.0770 chunk 616 optimal weight: 0.9980 chunk 376 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 428 optimal weight: 0.8980 chunk 646 optimal weight: 3.9990 chunk 595 optimal weight: 5.9990 chunk 514 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 397 optimal weight: 1.9990 chunk 315 optimal weight: 0.0270 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS D 179 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN N 69 ASN O 103 ASN P 104 GLN Q 97 GLN Q 114 GLN R 62 GLN T 117 GLN T 142 ASN V 47 ASN W 15 ASN Z 89 GLN a 43 ASN b 29 ASN c 29 GLN j 158 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 80580 Z= 0.142 Angle : 0.554 14.792 116925 Z= 0.287 Chirality : 0.036 0.252 14442 Planarity : 0.004 0.072 8511 Dihedral : 22.773 179.636 32102 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.15 % Allowed : 16.94 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.82 (0.12), residues: 4844 helix: 1.84 (0.13), residues: 1628 sheet: 0.35 (0.17), residues: 929 loop : -0.26 (0.13), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP g 132 HIS 0.004 0.001 HIS Z 103 PHE 0.024 0.001 PHE b 79 TYR 0.015 0.001 TYR J 35 ARG 0.011 0.000 ARG V 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9688 Ramachandran restraints generated. 4844 Oldfield, 0 Emsley, 4844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 574 time to evaluate : 4.609 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: A 36 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: A 40 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8429 (tmtp) REVERT: B 113 MET cc_start: 0.8110 (mtp) cc_final: 0.7883 (mtm) REVERT: B 147 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7410 (t0) REVERT: B 229 MET cc_start: 0.8244 (mmt) cc_final: 0.7786 (mpm) REVERT: D 120 TYR cc_start: 0.7699 (m-80) cc_final: 0.7440 (m-80) REVERT: D 206 ASP cc_start: 0.8066 (p0) cc_final: 0.7804 (p0) REVERT: G 22 ARG cc_start: 0.7371 (mpp80) cc_final: 0.7133 (mtm-85) REVERT: G 148 SER cc_start: 0.7330 (p) cc_final: 0.6630 (t) REVERT: H 32 MET cc_start: 0.6353 (mmt) cc_final: 0.5880 (ptp) REVERT: H 81 ARG cc_start: 0.6717 (ttp-170) cc_final: 0.6074 (tpm170) REVERT: I 99 ASN cc_start: 0.8752 (t0) cc_final: 0.8291 (t160) REVERT: J 34 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7086 (tm-30) REVERT: K 77 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7439 (mm-40) REVERT: O 129 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8498 (mm) REVERT: O 138 ASP cc_start: 0.5863 (m-30) cc_final: 0.5547 (m-30) REVERT: P 136 THR cc_start: 0.6180 (m) cc_final: 0.5959 (p) REVERT: R 103 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8099 (tttp) REVERT: S 8 LYS cc_start: 0.8242 (pmtt) cc_final: 0.7691 (pttp) REVERT: S 14 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7496 (tmt-80) REVERT: V 21 ASN cc_start: 0.8547 (t0) cc_final: 0.8220 (t0) REVERT: V 50 PHE cc_start: 0.8335 (p90) cc_final: 0.8062 (p90) REVERT: b 3 LEU cc_start: 0.8751 (mp) cc_final: 0.8501 (mt) REVERT: c 35 MET cc_start: 0.8193 (mmm) cc_final: 0.7815 (mtm) REVERT: g 269 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.5932 (tm-30) outliers start: 91 outliers final: 73 residues processed: 629 average time/residue: 1.7042 time to fit residues: 1407.0189 Evaluate side-chains 641 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 561 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 219 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 29 GLU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 172 THR Chi-restraints excluded: chain H residue 174 SER Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 34 GLU Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 122 SER Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain K residue 59 LYS Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 146 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 129 ILE Chi-restraints excluded: chain P residue 21 ASP Chi-restraints excluded: chain Q residue 72 VAL Chi-restraints excluded: chain R residue 5 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 14 ARG Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 ILE Chi-restraints excluded: chain S residue 131 VAL Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 54 VAL Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain U residue 104 ILE Chi-restraints excluded: chain U residue 115 THR Chi-restraints excluded: chain W residue 15 ASN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 74 VAL Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 105 PHE Chi-restraints excluded: chain Y residue 50 THR Chi-restraints excluded: chain Y residue 109 GLU Chi-restraints excluded: chain Z residue 49 LEU Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 69 THR Chi-restraints excluded: chain Z residue 75 GLU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain b residue 6 ASP Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain f residue 102 VAL Chi-restraints excluded: chain f residue 126 CYS Chi-restraints excluded: chain g residue 51 ASN Chi-restraints excluded: chain g residue 113 PHE Chi-restraints excluded: chain g residue 132 TRP Chi-restraints excluded: chain g residue 165 ILE Chi-restraints excluded: chain g residue 266 ILE Chi-restraints excluded: chain g residue 269 GLU Chi-restraints excluded: chain g residue 309 VAL Chi-restraints excluded: chain j residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 649 random chunks: chunk 408 optimal weight: 1.9990 chunk 548 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 474 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 chunk 515 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 529 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 HIS D 179 GLN ** F 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN I 7 ASN N 69 ASN P 24 GLN P 104 GLN Q 97 GLN R 62 GLN T 117 GLN T 142 ASN U 81 GLN V 47 ASN W 15 ASN Z 89 GLN a 43 ASN b 29 ASN c 29 GLN j 158 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.077532 restraints weight = 152389.069| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.24 r_work: 0.2970 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 80580 Z= 0.164 Angle : 0.538 12.676 116925 Z= 0.278 Chirality : 0.036 0.247 14442 Planarity : 0.004 0.070 8511 Dihedral : 22.675 179.840 32102 Min Nonbonded Distance : 1.148 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.17 % Allowed : 16.99 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % 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: 0.88 (0.12), residues: 4844 helix: 1.89 (0.13), residues: 1631 sheet: 0.35 (0.17), residues: 919 loop : -0.22 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP g 132 HIS 0.004 0.001 HIS Y 89 PHE 0.026 0.001 PHE b 79 TYR 0.014 0.001 TYR M 61 ARG 0.010 0.000 ARG V 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23883.11 seconds wall clock time: 410 minutes 58.29 seconds (24658.29 seconds total)