Starting phenix.real_space_refine (version: dev) on Thu Dec 15 06:19:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zv6_11441/12_2022/6zv6_11441_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "O ARG 149": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "a ARG 87": "NH1" <-> "NH2" Residue "a ARG 89": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T ARG 84": "NH1" <-> "NH2" Residue "T ARG 102": "NH1" <-> "NH2" Residue "T ARG 121": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 76226 Number of models: 1 Model: "" Number of chains: 38 Chain: "2" Number of atoms: 35903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1683, 35903 Inner-chain residues flagged as termini: ['pdbres=" U 2 140 "', 'pdbres=" U 2 287 "', 'pdbres=" G 2 329 "', 'pdbres=" C 2 746 "', 'pdbres=" C 2 791 "', 'pdbres=" G 2 841 "', 'pdbres=" G 21771 "'] Classifications: {'RNA': 1683} Modifications used: {'5*END': 8, 'rna2p': 1, 'rna2p_pur': 131, 'rna2p_pyr': 113, 'rna3p': 1, 'rna3p_pur': 757, 'rna3p_pyr': 680} Link IDs: {'rna2p': 244, 'rna3p': 1438} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 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: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'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: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} 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: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Modifications used: {'COO': 1} 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: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "Q" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "R" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 992 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} 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: "a" Number of atoms: 829 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 821 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Conformer: "B" Number of residues, atoms: 102, 821 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} bond proxies already assigned to first conformer: 827 Chain: "U" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "V" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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': 1, 'PTRANS': 2, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, '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: "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: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "e" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 442 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "f" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 510 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} 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: "T" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "h" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1775 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHD:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 7 Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2, 'water': 3} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 62536 SG CYS a 23 65.655 168.028 80.270 1.00102.11 S ATOM 62557 SG CYS a 26 68.118 168.009 77.644 1.00103.33 S ATOM 62940 SG CYS a 74 69.612 166.868 80.676 1.00105.23 S ATOM 62959 SG CYS a 77 69.717 170.413 79.768 1.00109.68 S Time building chain proxies: 32.43, per 1000 atoms: 0.43 Number of scatterers: 76226 At special positions: 0 Unit cell: (215.28, 282.88, 184.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 192 16.00 P 1678 15.00 Mg 3 11.99 O 18842 8.00 N 14009 7.00 C 41501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.89 Conformation dependent library (CDL) restraints added in 4.8 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 " Number of angles added : 6 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 56 sheets defined 29.0% alpha, 14.5% beta 498 base pairs and 886 stacking pairs defined. Time for finding SS restraints: 26.10 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 81 through 94 removed outlier: 3.618A pdb=" N GLN A 84 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA A 86 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 89 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA A 92 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 177 removed outlier: 4.681A pdb=" N VAL B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 189 removed outlier: 3.553A pdb=" N VAL B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 removed outlier: 4.614A pdb=" N SER B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 147 through 160 removed outlier: 3.512A pdb=" N ILE C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 217 removed outlier: 3.716A pdb=" N LYS C 212 " --> pdb=" O PRO C 208 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 247 removed outlier: 4.227A pdb=" N THR C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 265 through 268 No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'D' and resid 7 through 28 Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 98 through 110 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 248 through 261 Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 108 through 117 Processing helix chain 'F' and resid 143 through 160 Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'F' and resid 188 through 202 removed outlier: 3.669A pdb=" N LYS F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 153 through 156 Processing helix chain 'G' and resid 184 through 229 removed outlier: 3.620A pdb=" N ALA G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN G 227 " --> pdb=" O LYS G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 30 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.953A pdb=" N VAL H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 134 removed outlier: 4.248A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 180 removed outlier: 3.812A pdb=" N TYR H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS H 178 " --> pdb=" O SER H 174 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS H 179 " --> pdb=" O GLY H 175 " (cutoff:3.500A) 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 89 through 92 No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 107 through 116 Processing helix chain 'I' and resid 131 through 137 Processing helix chain 'I' and resid 143 through 152 Processing helix chain 'I' and resid 160 through 168 removed outlier: 4.146A pdb=" N GLU I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 205 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 62 removed outlier: 4.145A pdb=" N ARG J 45 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU J 59 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR J 62 " --> pdb=" O GLU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 94 through 97 No H-bonds generated for 'chain 'J' and resid 94 through 97' Processing helix chain 'J' and resid 102 through 106 Processing helix chain 'J' and resid 110 through 116 Processing helix chain 'J' and resid 123 through 131 Processing helix chain 'J' and resid 152 through 155 removed outlier: 4.090A pdb=" N LYS J 155 " --> pdb=" O ASP J 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 155' Processing helix chain 'J' and resid 172 through 180 removed outlier: 3.579A pdb=" N LYS J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 18 removed outlier: 3.567A pdb=" N ILE K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 14 " --> pdb=" O ALA K 10 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU K 15 " --> pdb=" O ILE K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 73 through 80 Processing helix chain 'L' and resid 24 through 27 removed outlier: 3.599A pdb=" N GLU L 27 " --> pdb=" O LEU L 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 24 through 27' Processing helix chain 'L' and resid 48 through 51 No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'M' and resid 14 through 27 removed outlier: 4.101A pdb=" N LEU M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLN M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 42 Processing helix chain 'M' and resid 59 through 71 removed outlier: 3.594A pdb=" N VAL M 65 " --> pdb=" O TYR M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 30 through 43 Processing helix chain 'N' and resid 47 through 56 Processing helix chain 'N' and resid 63 through 66 No H-bonds generated for 'chain 'N' and resid 63 through 66' Processing helix chain 'N' and resid 71 through 78 removed outlier: 3.704A pdb=" N LYS N 78 " --> pdb=" O ILE N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 102 Processing helix chain 'N' and resid 109 through 131 removed outlier: 3.937A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR N 131 " --> pdb=" O ARG N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 149 removed outlier: 4.037A pdb=" N SER N 147 " --> pdb=" O SER N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 71 through 88 Processing helix chain 'O' and resid 110 through 122 removed outlier: 4.243A pdb=" N SER O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 27 Processing helix chain 'P' and resid 31 through 34 No H-bonds generated for 'chain 'P' and resid 31 through 34' Processing helix chain 'P' and resid 39 through 46 Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 87 through 89 No H-bonds generated for 'chain 'P' and resid 87 through 89' Processing helix chain 'P' and resid 116 through 118 No H-bonds generated for 'chain 'P' and resid 116 through 118' Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 45 through 63 removed outlier: 4.784A pdb=" N TYR Q 49 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU Q 53 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Proline residue: Q 54 - end of helix removed outlier: 4.622A pdb=" N GLY Q 59 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LYS Q 60 " --> pdb=" O LEU Q 57 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU Q 61 " --> pdb=" O LEU Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.862A pdb=" N LYS Q 98 " --> pdb=" O ALA Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 115 removed outlier: 3.804A pdb=" N ILE Q 111 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'R' and resid 7 through 19 removed outlier: 3.713A pdb=" N ILE R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 38 removed outlier: 4.288A pdb=" N GLU R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 63 Processing helix chain 'R' and resid 74 through 81 removed outlier: 4.310A pdb=" N GLU R 79 " --> pdb=" O GLU R 75 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG R 81 " --> pdb=" O GLU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 108 Processing helix chain 'S' and resid 26 through 29 No H-bonds generated for 'chain 'S' and resid 26 through 29' Processing helix chain 'S' and resid 38 through 47 Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 100 through 117 removed outlier: 3.653A pdb=" N ASP S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN S 105 " --> pdb=" O ASN S 101 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP S 110 " --> pdb=" O LYS S 106 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 127 Processing helix chain 'a' and resid 47 through 53 removed outlier: 4.261A pdb=" N ARG a 51 " --> pdb=" O ALA a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 80 No H-bonds generated for 'chain 'a' and resid 77 through 80' Processing helix chain 'a' and resid 89 through 92 No H-bonds generated for 'chain 'a' and resid 89 through 92' Processing helix chain 'U' and resid 29 through 43 Processing helix chain 'U' and resid 95 through 102 removed outlier: 3.757A pdb=" N LYS U 99 " --> pdb=" O SER U 95 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN U 100 " --> pdb=" O GLU U 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 62 Processing helix chain 'V' and resid 65 through 75 removed outlier: 3.564A pdb=" N ARG V 71 " --> pdb=" O ASP V 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 20 Processing helix chain 'W' and resid 32 through 44 Processing helix chain 'W' and resid 85 through 92 removed outlier: 3.667A pdb=" N TRP W 89 " --> pdb=" O LEU W 86 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN W 92 " --> pdb=" O TRP W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 removed outlier: 3.563A pdb=" N ARG W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 23 removed outlier: 3.895A pdb=" N ASP X 19 " --> pdb=" O SER X 15 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 31 Processing helix chain 'X' and resid 35 through 38 No H-bonds generated for 'chain 'X' and resid 35 through 38' Processing helix chain 'X' and resid 90 through 93 Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 37 through 47 removed outlier: 3.593A pdb=" N GLU Y 42 " --> pdb=" O THR Y 38 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 84 Processing helix chain 'Y' and resid 88 through 94 removed outlier: 3.772A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 116 removed outlier: 4.103A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 64 No H-bonds generated for 'chain 'Z' and resid 62 through 64' Processing helix chain 'Z' and resid 70 through 76 Processing helix chain 'Z' and resid 81 through 93 removed outlier: 3.913A pdb=" N ARG Z 85 " --> pdb=" O GLY Z 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'd' and resid 40 through 50 removed outlier: 5.312A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 15 Processing helix chain 'e' and resid 30 through 41 removed outlier: 4.022A pdb=" N GLN e 37 " --> pdb=" O ARG e 34 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR e 38 " --> pdb=" O ARG e 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 105 No H-bonds generated for 'chain 'f' and resid 102 through 105' Processing helix chain 'T' and resid 12 through 23 Processing helix chain 'T' and resid 52 through 65 Processing helix chain 'T' and resid 73 through 77 removed outlier: 3.856A pdb=" N LYS T 77 " --> pdb=" O GLY T 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 73 through 77' Processing helix chain 'T' and resid 98 through 109 Processing helix chain 'T' and resid 125 through 133 Processing helix chain 'T' and resid 135 through 141 removed outlier: 3.657A pdb=" N ALA T 139 " --> pdb=" O ALA T 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 164 through 176 removed outlier: 3.576A pdb=" N MET h 168 " --> pdb=" O PRO h 164 " (cutoff:3.500A) Processing helix chain 'h' and resid 247 through 259 removed outlier: 3.840A pdb=" N ARG h 252 " --> pdb=" O GLU h 248 " (cutoff:3.500A) Processing helix chain 'h' and resid 290 through 292 No H-bonds generated for 'chain 'h' and resid 290 through 292' Processing helix chain 'h' and resid 297 through 316 Processing helix chain 'h' and resid 327 through 329 No H-bonds generated for 'chain 'h' and resid 327 through 329' Processing helix chain 'h' and resid 353 through 370 Processing helix chain 'h' and resid 378 through 386 Processing helix chain 'h' and resid 394 through 408 removed outlier: 3.608A pdb=" N GLN h 408 " --> pdb=" O GLU h 404 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 415 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 100 removed outlier: 5.836A pdb=" N LEU A 121 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE A 77 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL A 123 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 159 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS A 148 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 161 " --> pdb=" O CYS A 148 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.369A pdb=" N CYS B 96 " --> pdb=" O TRP B 30 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP B 32 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.509A pdb=" N LEU B 86 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 69 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 120 through 128 removed outlier: 6.623A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 136 through 144 removed outlier: 3.547A pdb=" N GLY C 119 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 184 through 187 Processing sheet with id= G, first strand: chain 'D' and resid 84 through 87 removed outlier: 6.700A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N TYR D 87 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 48 " --> pdb=" O TYR D 87 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 148 through 150 removed outlier: 3.592A pdb=" N GLY D 140 " --> pdb=" O LYS D 148 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 70 through 72 removed outlier: 4.218A pdb=" N ASP E 88 " --> pdb=" O LEU E 101 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 121 through 125 Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 Processing sheet with id= L, first strand: chain 'E' and resid 225 through 227 removed outlier: 6.720A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 123 through 127 Processing sheet with id= N, first strand: chain 'G' and resid 13 through 17 removed outlier: 3.784A pdb=" N LEU G 111 " --> pdb=" O ASN G 4 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE G 113 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= P, first strand: chain 'G' and resid 54 through 57 removed outlier: 3.656A pdb=" N GLY G 54 " --> pdb=" O ASN G 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 92 through 96 removed outlier: 6.646A pdb=" N ILE H 60 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE H 95 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE H 62 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE H 51 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 184 through 189 removed outlier: 4.613A pdb=" N ASP H 184 " --> pdb=" O ARG H 152 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 62 through 67 removed outlier: 3.513A pdb=" N GLY I 63 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 170 through 174 removed outlier: 6.631A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 42 through 47 removed outlier: 6.933A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 135 through 137 Processing sheet with id= W, first strand: chain 'K' and resid 58 through 62 Processing sheet with id= X, first strand: chain 'L' and resid 101 through 112 removed outlier: 6.297A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.765A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 16.893A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 31 through 33 Processing sheet with id= Z, first strand: chain 'M' and resid 51 through 53 removed outlier: 6.292A pdb=" N ILE M 77 " --> pdb=" O LEU M 52 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'O' and resid 52 through 57 removed outlier: 6.832A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL O 30 " --> pdb=" O THR O 45 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= AC, first strand: chain 'Q' and resid 10 through 14 Processing sheet with id= AD, first strand: chain 'R' and resid 96 through 98 Processing sheet with id= AE, first strand: chain 'S' and resid 12 through 15 Processing sheet with id= AF, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= AG, first strand: chain 'a' and resid 36 through 40 Processing sheet with id= AH, first strand: chain 'U' and resid 20 through 26 removed outlier: 3.655A pdb=" N HIS U 92 " --> pdb=" O LYS U 49 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS U 49 " --> pdb=" O HIS U 92 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 59 through 66 Processing sheet with id= AJ, first strand: chain 'V' and resid 34 through 37 Processing sheet with id= AK, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AL, first strand: chain 'W' and resid 71 through 74 Processing sheet with id= AM, first strand: chain 'X' and resid 80 through 84 removed outlier: 3.542A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id= AO, first strand: chain 'Z' and resid 98 through 101 removed outlier: 6.762A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'c' and resid 19 through 21 Processing sheet with id= AQ, first strand: chain 'c' and resid 14 through 17 removed outlier: 6.729A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'f' and resid 106 through 109 removed outlier: 4.073A pdb=" N ASP f 109 " --> pdb=" O LYS f 113 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS f 113 " --> pdb=" O ASP f 109 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'f' and resid 132 through 134 removed outlier: 3.545A pdb=" N TYR f 140 " --> pdb=" O ALA f 133 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'g' and resid 4 through 7 Processing sheet with id= AU, first strand: chain 'g' and resid 18 through 22 removed outlier: 6.875A pdb=" N ALA g 34 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ILE g 21 " --> pdb=" O LEU g 32 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU g 32 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR g 39 " --> pdb=" O SER g 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG g 57 " --> pdb=" O MET g 42 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYS g 44 " --> pdb=" O PRO g 55 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'g' and resid 69 through 71 removed outlier: 4.112A pdb=" N ALA g 78 " --> pdb=" O TRP g 90 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASP g 91 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N THR g 97 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'g' and resid 154 through 156 removed outlier: 3.695A pdb=" N VAL g 174 " --> pdb=" O HIS g 188 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'g' and resid 229 through 231 removed outlier: 5.417A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 238 through 241 removed outlier: 3.793A pdb=" N ALA g 238 " --> pdb=" O ALA g 251 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP g 260 " --> pdb=" O ILE g 266 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE g 266 " --> pdb=" O ASP g 260 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'g' and resid 108 through 112 removed outlier: 6.942A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'T' and resid 80 through 83 Processing sheet with id= BB, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= BC, first strand: chain 'h' and resid 195 through 198 Processing sheet with id= BD, first strand: chain 'h' and resid 330 through 333 1214 hydrogen bonds defined for protein. 3372 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1244 hydrogen bonds 1972 hydrogen bond angles 0 basepair planarities 498 basepair parallelities 886 stacking parallelities Total time for adding SS restraints: 62.56 Time building geometry restraints manager: 33.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8952 1.31 - 1.43: 31065 1.43 - 1.56: 37486 1.56 - 1.69: 3358 1.69 - 1.81: 295 Bond restraints: 81156 Sorted by residual: bond pdb=" C3' ADP h 601 " pdb=" C4' ADP h 601 " ideal model delta sigma weight residual 1.524 1.297 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4' ADP h 601 " pdb=" O4' ADP h 601 " ideal model delta sigma weight residual 1.426 1.611 -0.185 2.00e-02 2.50e+03 8.58e+01 bond pdb=" OD1 PHD h 341 " pdb=" P PHD h 341 " ideal model delta sigma weight residual 1.816 1.650 0.166 2.00e-02 2.50e+03 6.90e+01 bond pdb=" C4 ADP h 601 " pdb=" C5 ADP h 601 " ideal model delta sigma weight residual 1.490 1.331 0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C1' ADP h 601 " pdb=" O4' ADP h 601 " ideal model delta sigma weight residual 1.426 1.302 0.124 2.00e-02 2.50e+03 3.82e+01 ... (remaining 81151 not shown) Histogram of bond angle deviations from ideal: 54.10 - 72.62: 1 72.62 - 91.14: 0 91.14 - 109.66: 28246 109.66 - 128.18: 86621 128.18 - 146.70: 2761 Bond angle restraints: 117629 Sorted by residual: angle pdb=" O3' A 21831 " pdb=" P 6MZ 21832 " pdb=" O1P 6MZ 21832 " ideal model delta sigma weight residual 108.00 54.10 53.90 3.00e+00 1.11e-01 3.23e+02 angle pdb=" O3' A 21831 " pdb=" P 6MZ 21832 " pdb=" O2P 6MZ 21832 " ideal model delta sigma weight residual 108.00 146.70 -38.70 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C3' A 21831 " pdb=" O3' A 21831 " pdb=" P 6MZ 21832 " ideal model delta sigma weight residual 120.20 107.79 12.41 1.50e+00 4.44e-01 6.84e+01 angle pdb=" N ILE B 150 " pdb=" CA ILE B 150 " pdb=" C ILE B 150 " ideal model delta sigma weight residual 113.43 104.61 8.82 1.09e+00 8.42e-01 6.55e+01 angle pdb=" N VAL C 274 " pdb=" CA VAL C 274 " pdb=" C VAL C 274 " ideal model delta sigma weight residual 113.53 105.63 7.90 9.80e-01 1.04e+00 6.50e+01 ... (remaining 117624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 43902 35.95 - 71.90: 1436 71.90 - 107.85: 133 107.85 - 143.80: 21 143.80 - 179.75: 42 Dihedral angle restraints: 45534 sinusoidal: 31004 harmonic: 14530 Sorted by residual: dihedral pdb=" CA ARG W 28 " pdb=" C ARG W 28 " pdb=" N PRO W 29 " pdb=" CA PRO W 29 " ideal model delta harmonic sigma weight residual -180.00 -119.17 -60.83 0 5.00e+00 4.00e-02 1.48e+02 dihedral pdb=" C4' C 21440 " pdb=" C3' C 21440 " pdb=" C2' C 21440 " pdb=" C1' C 21440 " ideal model delta sinusoidal sigma weight residual -35.00 29.99 -64.99 1 8.00e+00 1.56e-02 8.66e+01 dihedral pdb=" O4' U 21662 " pdb=" C1' U 21662 " pdb=" N1 U 21662 " pdb=" C2 U 21662 " ideal model delta sinusoidal sigma weight residual -160.00 15.35 -175.35 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 45531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 13203 0.089 - 0.178: 1190 0.178 - 0.268: 86 0.268 - 0.357: 22 0.357 - 0.446: 8 Chirality restraints: 14509 Sorted by residual: chirality pdb=" C3' G 21648 " pdb=" C4' G 21648 " pdb=" O3' G 21648 " pdb=" C2' G 21648 " both_signs ideal model delta sigma weight residual False -2.74 -2.30 -0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" C3' G 21425 " pdb=" C4' G 21425 " pdb=" O3' G 21425 " pdb=" C2' G 21425 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" C3' U 21649 " pdb=" C4' U 21649 " pdb=" O3' U 21649 " pdb=" C2' U 21649 " both_signs ideal model delta sigma weight residual False -2.48 -2.07 -0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 14506 not shown) Planarity restraints: 8685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG W 28 " 0.095 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO W 29 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO W 29 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO W 29 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U 2 495 " 0.046 2.00e-02 2.50e+03 2.31e-02 1.20e+01 pdb=" N1 U 2 495 " -0.046 2.00e-02 2.50e+03 pdb=" C2 U 2 495 " -0.008 2.00e-02 2.50e+03 pdb=" O2 U 2 495 " -0.003 2.00e-02 2.50e+03 pdb=" N3 U 2 495 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U 2 495 " 0.005 2.00e-02 2.50e+03 pdb=" O4 U 2 495 " 0.017 2.00e-02 2.50e+03 pdb=" C5 U 2 495 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U 2 495 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21557 " -0.046 2.00e-02 2.50e+03 2.25e-02 1.14e+01 pdb=" N1 C 21557 " 0.021 2.00e-02 2.50e+03 pdb=" C2 C 21557 " 0.005 2.00e-02 2.50e+03 pdb=" O2 C 21557 " 0.020 2.00e-02 2.50e+03 pdb=" N3 C 21557 " -0.013 2.00e-02 2.50e+03 pdb=" C4 C 21557 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C 21557 " -0.013 2.00e-02 2.50e+03 pdb=" C5 C 21557 " -0.003 2.00e-02 2.50e+03 pdb=" C6 C 21557 " 0.035 2.00e-02 2.50e+03 ... (remaining 8682 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 3800 2.67 - 3.23: 64474 3.23 - 3.79: 147451 3.79 - 4.34: 189914 4.34 - 4.90: 269060 Nonbonded interactions: 674699 Sorted by model distance: nonbonded pdb="MG MG h 602 " pdb=" O HOH h 701 " model vdw 2.116 2.170 nonbonded pdb=" OH TYR P 37 " pdb=" O ILE P 112 " model vdw 2.191 2.440 nonbonded pdb=" O2A ADP h 601 " pdb="MG MG h 602 " model vdw 2.209 2.170 nonbonded pdb=" OD1 PHD h 341 " pdb="MG MG h 602 " model vdw 2.218 2.170 nonbonded pdb=" O SER g 157 " pdb=" OG SER g 160 " model vdw 2.234 2.440 ... (remaining 674694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1678 5.49 5 Mg 3 5.21 5 S 192 5.16 5 C 41501 2.51 5 N 14009 2.21 5 O 18842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.860 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: 15.730 Check model and map are aligned: 0.830 Convert atoms to be neutral: 0.500 Process input model: 220.540 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 255.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.008 0.227 81156 Z= 0.480 Angle : 1.068 53.904 117629 Z= 0.566 Chirality : 0.054 0.446 14509 Planarity : 0.007 0.145 8685 Dihedral : 15.859 179.748 36160 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.15 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.10), residues: 4976 helix: -2.62 (0.10), residues: 1563 sheet: -2.08 (0.16), residues: 853 loop : -2.13 (0.10), residues: 2560 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2284 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 2263 time to evaluate : 4.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 2270 average time/residue: 1.5420 time to fit residues: 4616.0629 Evaluate side-chains 1623 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1617 time to evaluate : 4.447 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 2 average time/residue: 1.6094 time to fit residues: 9.7863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 0.9990 chunk 500 optimal weight: 0.9990 chunk 277 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 337 optimal weight: 7.9990 chunk 267 optimal weight: 1.9990 chunk 517 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 314 optimal weight: 0.0570 chunk 385 optimal weight: 0.0980 chunk 599 optimal weight: 5.9990 overall best weight: 0.8304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 113 GLN A 164 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 145 GLN D 207 HIS E 8 HIS E 161 GLN E 188 ASN E 201 HIS E 209 HIS E 224 ASN F 31 ASN F 51 HIS F 65 GLN F 74 ASN F 83 ASN F 107 ASN F 110 GLN F 114 ASN G 13 GLN G 81 HIS G 202 ASN H 73 GLN H 126 HIS H 157 HIS H 163 GLN H 186 ASN ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 138 ASN ** I 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 GLN K 7 ASN L 5 GLN L 39 ASN L 65 ASN L 121 GLN M 72 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 83 GLN P 103 ASN Q 80 GLN R 26 ASN S 11 HIS ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 135 HIS a 8 ASN a 72 HIS ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 16 ASN W 56 HIS W 64 ASN W 70 ASN X 20 GLN X 87 ASN Z 45 ASN Z 46 ASN Z 64 ASN Z 103 HIS c 29 GLN c 45 ASN d 3 HIS d 26 ASN d 28 HIS d 45 GLN f 139 HIS g 76 GLN g 272 GLN T 63 HIS T 83 GLN h 193 ASN h 196 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 81156 Z= 0.199 Angle : 0.693 13.385 117629 Z= 0.355 Chirality : 0.040 0.319 14509 Planarity : 0.006 0.077 8685 Dihedral : 16.748 179.854 25769 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer Outliers : 5.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.11), residues: 4976 helix: -1.23 (0.12), residues: 1562 sheet: -1.62 (0.16), residues: 885 loop : -1.60 (0.11), residues: 2529 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2077 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1837 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 240 outliers final: 97 residues processed: 1901 average time/residue: 1.4575 time to fit residues: 3726.6648 Evaluate side-chains 1775 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1678 time to evaluate : 4.473 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 22 residues processed: 81 average time/residue: 0.8354 time to fit residues: 113.2952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 20.0000 chunk 186 optimal weight: 5.9990 chunk 498 optimal weight: 8.9990 chunk 408 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 600 optimal weight: 7.9990 chunk 648 optimal weight: 20.0000 chunk 534 optimal weight: 0.6980 chunk 595 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 481 optimal weight: 0.0980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 92 GLN B 163 GLN C 172 ASN ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN E 161 GLN E 224 ASN F 31 ASN F 65 GLN F 179 ASN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 HIS ** H 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 167 GLN K 39 ASN L 5 GLN L 65 ASN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Q 11 GLN Q 29 ASN S 11 HIS ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 ASN W 56 HIS W 64 ASN X 20 GLN X 63 ASN b 49 HIS d 26 ASN e 15 GLN e 44 ASN g 14 HIS ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN h 253 ASN h 363 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 81156 Z= 0.295 Angle : 0.696 11.120 117629 Z= 0.356 Chirality : 0.042 0.292 14509 Planarity : 0.005 0.083 8685 Dihedral : 16.598 179.141 25769 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.69 % Favored : 94.19 % Rotamer Outliers : 6.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.11), residues: 4976 helix: -0.50 (0.12), residues: 1535 sheet: -1.43 (0.16), residues: 892 loop : -1.31 (0.12), residues: 2549 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2025 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1732 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 293 outliers final: 149 residues processed: 1816 average time/residue: 1.4487 time to fit residues: 3538.4479 Evaluate side-chains 1776 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1627 time to evaluate : 4.522 Switching outliers to nearest non-outliers outliers start: 149 outliers final: 45 residues processed: 107 average time/residue: 0.7399 time to fit residues: 138.7016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 8.9990 chunk 451 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 chunk 403 optimal weight: 10.0000 chunk 602 optimal weight: 3.9990 chunk 637 optimal weight: 2.9990 chunk 314 optimal weight: 7.9990 chunk 571 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN C 134 ASN C 235 ASN D 145 GLN E 161 GLN E 224 ASN F 31 ASN F 65 GLN G 70 HIS G 163 ASN I 99 ASN K 39 ASN L 5 GLN L 65 ASN M 19 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN Q 11 GLN Q 29 ASN S 11 HIS a 72 HIS U 18 HIS ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 64 ASN X 20 GLN X 63 ASN X 127 ASN b 51 GLN d 26 ASN e 15 GLN ** g 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 81156 Z= 0.320 Angle : 0.705 10.853 117629 Z= 0.360 Chirality : 0.042 0.298 14509 Planarity : 0.005 0.083 8685 Dihedral : 16.560 179.786 25769 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.99 % Favored : 93.89 % Rotamer Outliers : 7.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.11), residues: 4976 helix: -0.27 (0.13), residues: 1528 sheet: -1.25 (0.17), residues: 869 loop : -1.18 (0.12), residues: 2579 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2023 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1678 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 345 outliers final: 179 residues processed: 1795 average time/residue: 1.4475 time to fit residues: 3504.5263 Evaluate side-chains 1780 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1601 time to evaluate : 4.454 Switching outliers to nearest non-outliers outliers start: 179 outliers final: 61 residues processed: 122 average time/residue: 0.7237 time to fit residues: 154.9161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 0.7980 chunk 362 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 475 optimal weight: 40.0000 chunk 263 optimal weight: 2.9990 chunk 544 optimal weight: 0.0570 chunk 440 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 325 optimal weight: 7.9990 chunk 572 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 157 GLN C 134 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN E 224 ASN F 31 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS I 99 ASN L 5 GLN L 121 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 GLN P 128 HIS Q 11 GLN Q 80 GLN S 11 HIS S 19 ASN a 72 HIS U 18 HIS W 64 ASN X 20 GLN X 63 ASN d 26 ASN d 37 ASN ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN T 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 81156 Z= 0.195 Angle : 0.661 11.275 117629 Z= 0.334 Chirality : 0.039 0.269 14509 Planarity : 0.005 0.078 8685 Dihedral : 16.428 179.459 25769 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.51 % Favored : 94.43 % Rotamer Outliers : 5.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.23 (0.12), residues: 4976 helix: -0.04 (0.13), residues: 1518 sheet: -1.16 (0.17), residues: 874 loop : -1.11 (0.12), residues: 2584 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1925 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1667 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 258 outliers final: 142 residues processed: 1780 average time/residue: 1.4492 time to fit residues: 3475.1398 Evaluate side-chains 1709 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1567 time to evaluate : 4.501 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 70 residues processed: 76 average time/residue: 0.7743 time to fit residues: 102.1102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 3.9990 chunk 574 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 374 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 638 optimal weight: 20.0000 chunk 530 optimal weight: 8.9990 chunk 295 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 335 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN B 118 GLN B 157 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN D 22 ASN E 161 GLN E 224 ASN F 31 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 HIS G 187 HIS H 73 GLN H 193 GLN I 99 ASN I 167 GLN K 39 ASN L 5 GLN L 65 ASN L 121 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 113 GLN Q 11 GLN Q 80 GLN ** R 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 HIS S 87 GLN a 72 HIS ** U 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN X 63 ASN Y 63 HIS Y 94 HIS d 26 ASN ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN T 83 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.102 81156 Z= 0.394 Angle : 0.755 10.955 117629 Z= 0.383 Chirality : 0.044 0.308 14509 Planarity : 0.006 0.083 8685 Dihedral : 16.478 179.887 25769 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.65 % Favored : 93.23 % Rotamer Outliers : 6.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.28 (0.11), residues: 4976 helix: -0.12 (0.13), residues: 1512 sheet: -1.15 (0.17), residues: 872 loop : -1.12 (0.12), residues: 2592 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1897 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1601 time to evaluate : 4.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 296 outliers final: 182 residues processed: 1715 average time/residue: 1.4385 time to fit residues: 3336.5106 Evaluate side-chains 1735 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1553 time to evaluate : 4.455 Switching outliers to nearest non-outliers outliers start: 182 outliers final: 78 residues processed: 111 average time/residue: 0.6786 time to fit residues: 135.9115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 363 optimal weight: 1.9990 chunk 466 optimal weight: 0.8980 chunk 361 optimal weight: 0.8980 chunk 537 optimal weight: 1.9990 chunk 356 optimal weight: 0.9980 chunk 636 optimal weight: 0.9990 chunk 398 optimal weight: 1.9990 chunk 387 optimal weight: 5.9990 chunk 293 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN E 224 ASN F 31 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 HIS I 99 ASN I 167 GLN K 39 ASN L 5 GLN L 121 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN P 35 GLN Q 11 GLN Q 80 GLN S 11 HIS S 19 ASN a 72 HIS ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN X 63 ASN b 49 HIS d 26 ASN d 37 ASN ** e 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 44 ASN ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN T 83 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.093 81156 Z= 0.190 Angle : 0.689 14.079 117629 Z= 0.346 Chirality : 0.039 0.271 14509 Planarity : 0.005 0.090 8685 Dihedral : 16.321 179.870 25769 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.39 % Favored : 94.55 % Rotamer Outliers : 4.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.13 (0.12), residues: 4976 helix: 0.03 (0.13), residues: 1514 sheet: -1.01 (0.17), residues: 866 loop : -1.08 (0.12), residues: 2596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1825 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1616 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 209 outliers final: 129 residues processed: 1716 average time/residue: 1.4605 time to fit residues: 3392.5910 Evaluate side-chains 1679 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1550 time to evaluate : 4.439 Switching outliers to nearest non-outliers outliers start: 129 outliers final: 73 residues processed: 62 average time/residue: 0.6662 time to fit residues: 78.0197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 2.9990 chunk 254 optimal weight: 0.7980 chunk 379 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 404 optimal weight: 7.9990 chunk 433 optimal weight: 0.0470 chunk 314 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 500 optimal weight: 9.9990 overall best weight: 2.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN D 22 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 31 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN G 202 ASN I 22 HIS I 88 ASN I 167 GLN K 39 ASN L 5 GLN L 65 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN O 83 GLN P 114 HIS Q 11 GLN ** R 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 72 HIS U 18 HIS W 24 GLN W 64 ASN X 20 GLN X 63 ASN c 29 GLN d 26 ASN ** e 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN T 105 GLN h 394 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.081 81156 Z= 0.283 Angle : 0.719 12.728 117629 Z= 0.362 Chirality : 0.041 0.301 14509 Planarity : 0.005 0.111 8685 Dihedral : 16.273 178.660 25769 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.27 % Favored : 93.65 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.11 (0.12), residues: 4976 helix: 0.01 (0.13), residues: 1509 sheet: -1.04 (0.17), residues: 897 loop : -1.02 (0.12), residues: 2570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1815 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1594 time to evaluate : 6.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 147 residues processed: 1691 average time/residue: 1.4490 time to fit residues: 3340.1399 Evaluate side-chains 1689 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1542 time to evaluate : 4.467 Switching outliers to nearest non-outliers outliers start: 147 outliers final: 80 residues processed: 79 average time/residue: 0.7758 time to fit residues: 108.3403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 6.9990 chunk 609 optimal weight: 0.8980 chunk 556 optimal weight: 10.0000 chunk 592 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 258 optimal weight: 4.9990 chunk 465 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 535 optimal weight: 0.9980 chunk 560 optimal weight: 5.9990 chunk 590 optimal weight: 0.0470 overall best weight: 1.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN D 22 ASN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 31 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN I 22 HIS K 39 ASN L 5 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN P 114 HIS Q 11 GLN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN U 18 HIS U 85 HIS V 21 ASN W 64 ASN X 20 GLN X 63 ASN b 83 GLN d 26 ASN d 37 ASN ** e 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 GLN h 196 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 81156 Z= 0.257 Angle : 0.720 13.783 117629 Z= 0.362 Chirality : 0.041 0.277 14509 Planarity : 0.005 0.111 8685 Dihedral : 16.246 178.837 25769 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer Outliers : 3.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.12 (0.12), residues: 4976 helix: -0.04 (0.13), residues: 1521 sheet: -1.02 (0.17), residues: 903 loop : -1.01 (0.12), residues: 2552 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1563 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 120 residues processed: 1659 average time/residue: 1.4383 time to fit residues: 3229.5403 Evaluate side-chains 1655 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1535 time to evaluate : 4.426 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 82 residues processed: 50 average time/residue: 0.6905 time to fit residues: 65.1086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 5.9990 chunk 626 optimal weight: 0.8980 chunk 382 optimal weight: 0.8980 chunk 297 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 657 optimal weight: 0.6980 chunk 605 optimal weight: 5.9990 chunk 523 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 404 optimal weight: 0.3980 chunk 321 optimal weight: 20.0000 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 157 GLN ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 ASN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 31 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN I 22 HIS I 167 GLN L 5 GLN L 65 ASN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS Q 11 GLN ** R 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 HIS V 21 ASN W 64 ASN X 20 GLN X 63 ASN Z 89 GLN c 29 GLN d 26 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 HIS g 187 ASN g 188 HIS T 83 GLN T 126 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 81156 Z= 0.229 Angle : 0.725 16.192 117629 Z= 0.362 Chirality : 0.040 0.266 14509 Planarity : 0.005 0.102 8685 Dihedral : 16.183 179.240 25769 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.01 % Favored : 93.93 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.12), residues: 4976 helix: -0.07 (0.13), residues: 1512 sheet: -0.96 (0.17), residues: 885 loop : -0.98 (0.12), residues: 2579 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9952 Ramachandran restraints generated. 4976 Oldfield, 0 Emsley, 4976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1582 time to evaluate : 4.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 111 residues processed: 1663 average time/residue: 1.4745 time to fit residues: 3312.4419 Evaluate side-chains 1631 residues out of total 4355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1520 time to evaluate : 4.429 Switching outliers to nearest non-outliers outliers start: 111 outliers final: 78 residues processed: 40 average time/residue: 0.7732 time to fit residues: 56.5703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 2.9990 chunk 557 optimal weight: 0.3980 chunk 160 optimal weight: 7.9990 chunk 482 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 524 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 538 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN D 22 ASN ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 31 ASN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 HIS I 167 GLN J 132 GLN L 5 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN O 83 GLN P 114 HIS Q 11 GLN ** Q 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 ASN S 134 GLN U 18 HIS V 21 ASN W 64 ASN X 20 GLN X 63 ASN Z 89 GLN c 29 GLN d 26 ASN ** g 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 HIS T 83 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.133574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100810 restraints weight = 173463.276| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.32 r_work: 0.3173 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3769 r_free = 0.3769 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 41 | |-----------------------------------------------------------------------------| r_final: 0.3769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 81156 Z= 0.222 Angle : 0.728 25.426 117629 Z= 0.361 Chirality : 0.040 0.431 14509 Planarity : 0.005 0.090 8685 Dihedral : 16.132 179.099 25769 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.05 % Favored : 93.89 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.50 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -1.09 (0.12), residues: 4976 helix: -0.07 (0.13), residues: 1510 sheet: -1.01 (0.17), residues: 890 loop : -0.94 (0.12), residues: 2576 =============================================================================== Job complete usr+sys time: 43773.98 seconds wall clock time: 752 minutes 43.78 seconds (45163.78 seconds total)