Starting phenix.real_space_refine (version: dev) on Sat Apr 9 08:38:54 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/04_2022/6z80_11113_updated.pdb" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 21460 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "L" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "B" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "C" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "G" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "H" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "I" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "J" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "F" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "D" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1432 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "K" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "N" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "M" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "O" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "P" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "Q" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "R" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "S" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 1} Chain: "T" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 77, 'PCIS': 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: "L" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'8GT': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'8GT': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'8GT': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'8GT': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'8GT': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'8GT': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'8GT': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'8GT': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "N" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "Q" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 579 SG CYS A 141 66.209 29.161 63.192 1.00 0.00 S ATOM 1133 SG CYS A 212 68.433 32.356 65.361 1.00 0.00 S ATOM 2680 SG CYS B 141 85.293 60.978 63.219 1.00 0.00 S ATOM 3234 SG CYS B 212 82.941 64.065 65.410 1.00 0.00 S ATOM 4112 SG CYS C 141 60.877 88.927 63.261 1.00 0.00 S ATOM 4666 SG CYS C 212 57.215 87.640 65.450 1.00 0.00 S ATOM 5544 SG CYS E 141 30.126 37.333 63.246 1.00 0.00 S ATOM 6098 SG CYS E 212 33.850 36.219 65.426 1.00 0.00 S ATOM 6976 SG CYS G 141 26.769 41.963 83.186 1.00 0.00 S ATOM 7530 SG CYS G 212 26.862 45.843 80.996 1.00 0.00 S ATOM 8408 SG CYS H 141 30.052 78.969 83.215 1.00 0.00 S ATOM 8962 SG CYS H 212 33.766 80.090 81.022 1.00 0.00 S ATOM 9840 SG CYS I 141 66.290 87.163 83.194 1.00 0.00 S ATOM 10394 SG CYS I 212 68.508 83.971 81.014 1.00 0.00 S ATOM 11272 SG CYS J 141 85.271 55.282 83.234 1.00 0.00 S ATOM 11826 SG CYS J 212 82.910 52.202 81.042 1.00 0.00 S ATOM 12704 SG CYS F 141 60.807 27.315 83.262 1.00 0.00 S ATOM 13258 SG CYS F 212 57.149 28.614 81.073 1.00 0.00 S ATOM 14136 SG CYS D 141 26.662 74.282 63.285 1.00 0.00 S ATOM 14690 SG CYS D 212 26.776 70.401 65.473 1.00 0.00 S Time building chain proxies: 12.29, per 1000 atoms: 0.57 Number of scatterers: 21460 At special positions: 0 Unit cell: (113.085, 117.393, 147.549, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 10 29.99 S 170 16.00 P 30 15.00 O 3990 8.00 N 3740 7.00 C 13520 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: 8.43 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 212 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 144 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 141 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 212 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 144 " pdb=" ZN C 302 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 302 " - pdb=" SG CYS C 212 " pdb="ZN ZN C 302 " - pdb=" ND1 HIS C 144 " pdb=" ZN D 303 " pdb="ZN ZN D 303 " - pdb=" SG CYS D 141 " pdb="ZN ZN D 303 " - pdb=" SG CYS D 212 " pdb="ZN ZN D 303 " - pdb=" ND1 HIS D 144 " pdb=" ZN E 302 " pdb="ZN ZN E 302 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 302 " - pdb=" SG CYS E 212 " pdb="ZN ZN E 302 " - pdb=" ND1 HIS E 144 " pdb=" ZN F 303 " pdb="ZN ZN F 303 " - pdb=" SG CYS F 141 " pdb="ZN ZN F 303 " - pdb=" SG CYS F 212 " pdb="ZN ZN F 303 " - pdb=" ND1 HIS F 144 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 141 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 212 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 144 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" SG CYS H 141 " pdb="ZN ZN H 302 " - pdb=" SG CYS H 212 " pdb="ZN ZN H 302 " - pdb=" ND1 HIS H 144 " pdb=" ZN I 302 " pdb="ZN ZN I 302 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 302 " - pdb=" SG CYS I 212 " pdb="ZN ZN I 302 " - pdb=" ND1 HIS I 144 " pdb=" ZN J 302 " pdb="ZN ZN J 302 " - pdb=" SG CYS J 141 " pdb="ZN ZN J 302 " - pdb=" SG CYS J 212 " pdb="ZN ZN J 302 " - pdb=" ND1 HIS J 144 " 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 50 sheets defined 37.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.904A pdb=" N SER A 100 " --> pdb=" O TRP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 165 through 176 removed outlier: 3.873A pdb=" N ALA A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 174 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.637A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 232 through 236 removed outlier: 4.096A pdb=" N GLU A 236 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 4.164A pdb=" N GLU A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 32 Processing helix chain 'L' and resid 53 through 63 removed outlier: 3.929A pdb=" N ARG L 62 " --> pdb=" O ASP L 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG L 63 " --> pdb=" O LYS L 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.904A pdb=" N SER B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 165 through 176 removed outlier: 3.874A pdb=" N ALA B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 174 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.637A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 189 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.096A pdb=" N GLU B 236 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 4.165A pdb=" N GLU B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 76 through 81 Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.903A pdb=" N SER C 100 " --> pdb=" O TRP C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.874A pdb=" N ALA C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.637A pdb=" N LYS C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 214 No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 232 through 236 removed outlier: 4.096A pdb=" N GLU C 236 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 4.165A pdb=" N GLU C 243 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 76 through 81 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 94 through 104 removed outlier: 3.904A pdb=" N SER E 100 " --> pdb=" O TRP E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 113 through 117 Processing helix chain 'E' and resid 165 through 176 removed outlier: 3.873A pdb=" N ALA E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU E 173 " --> pdb=" O ALA E 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.638A pdb=" N LYS E 187 " --> pdb=" O GLU E 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 214 No H-bonds generated for 'chain 'E' and resid 211 through 214' Processing helix chain 'E' and resid 232 through 236 removed outlier: 4.096A pdb=" N GLU E 236 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 removed outlier: 4.165A pdb=" N GLU E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE E 244 " --> pdb=" O THR E 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 Processing helix chain 'G' and resid 76 through 81 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 94 through 104 removed outlier: 3.904A pdb=" N SER G 100 " --> pdb=" O TRP G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'G' and resid 165 through 176 removed outlier: 3.874A pdb=" N ALA G 169 " --> pdb=" O LEU G 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU G 173 " --> pdb=" O ALA G 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 197 removed outlier: 3.637A pdb=" N LYS G 187 " --> pdb=" O GLU G 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE G 189 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 214 No H-bonds generated for 'chain 'G' and resid 211 through 214' Processing helix chain 'G' and resid 232 through 236 removed outlier: 4.096A pdb=" N GLU G 236 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 removed outlier: 4.165A pdb=" N GLU G 243 " --> pdb=" O LYS G 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE G 244 " --> pdb=" O THR G 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 74 Processing helix chain 'H' and resid 76 through 81 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 94 through 104 removed outlier: 3.903A pdb=" N SER H 100 " --> pdb=" O TRP H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'H' and resid 165 through 176 removed outlier: 3.874A pdb=" N ALA H 169 " --> pdb=" O LEU H 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL H 172 " --> pdb=" O LEU H 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU H 173 " --> pdb=" O ALA H 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE H 174 " --> pdb=" O ARG H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 197 removed outlier: 3.638A pdb=" N LYS H 187 " --> pdb=" O GLU H 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE H 189 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 214 No H-bonds generated for 'chain 'H' and resid 211 through 214' Processing helix chain 'H' and resid 232 through 236 removed outlier: 4.097A pdb=" N GLU H 236 " --> pdb=" O VAL H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 247 removed outlier: 4.164A pdb=" N GLU H 243 " --> pdb=" O LYS H 239 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE H 244 " --> pdb=" O THR H 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR H 246 " --> pdb=" O GLU H 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 Processing helix chain 'I' and resid 76 through 81 Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 94 through 104 removed outlier: 3.904A pdb=" N SER I 100 " --> pdb=" O TRP I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 110 No H-bonds generated for 'chain 'I' and resid 108 through 110' Processing helix chain 'I' and resid 113 through 117 Processing helix chain 'I' and resid 165 through 176 removed outlier: 3.874A pdb=" N ALA I 169 " --> pdb=" O LEU I 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU I 173 " --> pdb=" O ALA I 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 197 removed outlier: 3.637A pdb=" N LYS I 187 " --> pdb=" O GLU I 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE I 189 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 214 No H-bonds generated for 'chain 'I' and resid 211 through 214' Processing helix chain 'I' and resid 232 through 236 removed outlier: 4.097A pdb=" N GLU I 236 " --> pdb=" O VAL I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 247 removed outlier: 4.164A pdb=" N GLU I 243 " --> pdb=" O LYS I 239 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE I 244 " --> pdb=" O THR I 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR I 246 " --> pdb=" O GLU I 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 Processing helix chain 'J' and resid 76 through 81 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 94 through 104 removed outlier: 3.904A pdb=" N SER J 100 " --> pdb=" O TRP J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 113 through 117 Processing helix chain 'J' and resid 165 through 176 removed outlier: 3.874A pdb=" N ALA J 169 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE J 174 " --> pdb=" O ARG J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.637A pdb=" N LYS J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE J 189 " --> pdb=" O LEU J 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 214 No H-bonds generated for 'chain 'J' and resid 211 through 214' Processing helix chain 'J' and resid 232 through 236 removed outlier: 4.096A pdb=" N GLU J 236 " --> pdb=" O VAL J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 247 removed outlier: 4.166A pdb=" N GLU J 243 " --> pdb=" O LYS J 239 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE J 244 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR J 246 " --> pdb=" O GLU J 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 76 through 81 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 94 through 104 removed outlier: 3.904A pdb=" N SER F 100 " --> pdb=" O TRP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 165 through 176 removed outlier: 3.873A pdb=" N ALA F 169 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU F 173 " --> pdb=" O ALA F 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.637A pdb=" N LYS F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 214 No H-bonds generated for 'chain 'F' and resid 211 through 214' Processing helix chain 'F' and resid 232 through 236 removed outlier: 4.096A pdb=" N GLU F 236 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 247 removed outlier: 4.164A pdb=" N GLU F 243 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR F 246 " --> pdb=" O GLU F 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 76 through 81 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.903A pdb=" N SER D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 165 through 176 removed outlier: 3.874A pdb=" N ALA D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 173 " --> pdb=" O ALA D 169 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.638A pdb=" N LYS D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 214 No H-bonds generated for 'chain 'D' and resid 211 through 214' Processing helix chain 'D' and resid 232 through 236 removed outlier: 4.096A pdb=" N GLU D 236 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 removed outlier: 4.165A pdb=" N GLU D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 32 Processing helix chain 'K' and resid 53 through 63 removed outlier: 3.929A pdb=" N ARG K 62 " --> pdb=" O ASP K 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 32 Processing helix chain 'N' and resid 53 through 63 removed outlier: 3.929A pdb=" N ARG N 62 " --> pdb=" O ASP N 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG N 63 " --> pdb=" O LYS N 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 32 Processing helix chain 'M' and resid 53 through 63 removed outlier: 3.929A pdb=" N ARG M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG M 63 " --> pdb=" O LYS M 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 32 Processing helix chain 'O' and resid 53 through 63 removed outlier: 3.930A pdb=" N ARG O 62 " --> pdb=" O ASP O 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG O 63 " --> pdb=" O LYS O 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 32 Processing helix chain 'P' and resid 53 through 63 removed outlier: 3.929A pdb=" N ARG P 62 " --> pdb=" O ASP P 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG P 63 " --> pdb=" O LYS P 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 32 Processing helix chain 'Q' and resid 53 through 63 removed outlier: 3.929A pdb=" N ARG Q 62 " --> pdb=" O ASP Q 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Q 63 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 32 Processing helix chain 'R' and resid 53 through 63 removed outlier: 3.930A pdb=" N ARG R 62 " --> pdb=" O ASP R 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 32 Processing helix chain 'S' and resid 53 through 63 removed outlier: 3.930A pdb=" N ARG S 62 " --> pdb=" O ASP S 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 32 Processing helix chain 'T' and resid 53 through 63 removed outlier: 3.929A pdb=" N ARG T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG T 63 " --> pdb=" O LYS T 59 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 121 through 123 Processing sheet with id= B, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.508A pdb=" N VAL A 149 " --> pdb=" O THR A 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 201 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 135 through 140 Processing sheet with id= D, first strand: chain 'L' and resid 3 through 8 removed outlier: 3.514A pdb=" N SER L 69 " --> pdb=" O CYS L 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS L 82 " --> pdb=" O VAL L 67 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL L 67 " --> pdb=" O HIS L 82 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 35 through 37 removed outlier: 4.016A pdb=" N GLY L 20 " --> pdb=" O TYR L 47 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL L 49 " --> pdb=" O MET L 18 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N MET L 18 " --> pdb=" O VAL L 49 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 121 through 123 Processing sheet with id= G, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.508A pdb=" N VAL B 149 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 201 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 135 through 140 Processing sheet with id= I, first strand: chain 'C' and resid 121 through 123 Processing sheet with id= J, first strand: chain 'C' and resid 129 through 132 removed outlier: 3.509A pdb=" N VAL C 149 " --> pdb=" O THR C 209 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY C 201 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 135 through 140 Processing sheet with id= L, first strand: chain 'E' and resid 121 through 123 Processing sheet with id= M, first strand: chain 'E' and resid 129 through 132 removed outlier: 3.509A pdb=" N VAL E 149 " --> pdb=" O THR E 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY E 201 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 135 through 140 Processing sheet with id= O, first strand: chain 'G' and resid 121 through 123 Processing sheet with id= P, first strand: chain 'G' and resid 129 through 132 removed outlier: 3.509A pdb=" N VAL G 149 " --> pdb=" O THR G 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY G 201 " --> pdb=" O LEU G 157 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 135 through 140 Processing sheet with id= R, first strand: chain 'H' and resid 121 through 123 Processing sheet with id= S, first strand: chain 'H' and resid 129 through 132 removed outlier: 3.508A pdb=" N VAL H 149 " --> pdb=" O THR H 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY H 201 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 135 through 140 Processing sheet with id= U, first strand: chain 'I' and resid 121 through 123 Processing sheet with id= V, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.509A pdb=" N VAL I 149 " --> pdb=" O THR I 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY I 201 " --> pdb=" O LEU I 157 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 135 through 140 Processing sheet with id= X, first strand: chain 'J' and resid 121 through 123 Processing sheet with id= Y, first strand: chain 'J' and resid 129 through 132 removed outlier: 3.509A pdb=" N VAL J 149 " --> pdb=" O THR J 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY J 201 " --> pdb=" O LEU J 157 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 135 through 140 Processing sheet with id= AA, first strand: chain 'F' and resid 121 through 123 Processing sheet with id= AB, first strand: chain 'F' and resid 129 through 132 removed outlier: 3.508A pdb=" N VAL F 149 " --> pdb=" O THR F 209 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY F 201 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 135 through 140 Processing sheet with id= AD, first strand: chain 'D' and resid 121 through 123 Processing sheet with id= AE, first strand: chain 'D' and resid 129 through 132 removed outlier: 3.509A pdb=" N VAL D 149 " --> pdb=" O THR D 209 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY D 201 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'D' and resid 135 through 140 Processing sheet with id= AG, first strand: chain 'K' and resid 3 through 8 removed outlier: 3.514A pdb=" N SER K 69 " --> pdb=" O CYS K 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS K 82 " --> pdb=" O VAL K 67 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL K 67 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY K 20 " --> pdb=" O TYR K 47 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL K 49 " --> pdb=" O MET K 18 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N MET K 18 " --> pdb=" O VAL K 49 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.514A pdb=" N SER N 69 " --> pdb=" O CYS N 80 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS N 82 " --> pdb=" O VAL N 67 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL N 67 " --> pdb=" O HIS N 82 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY N 20 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL N 49 " --> pdb=" O MET N 18 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N MET N 18 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 3 through 8 removed outlier: 3.513A pdb=" N SER M 69 " --> pdb=" O CYS M 80 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS M 82 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL M 67 " --> pdb=" O HIS M 82 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY M 20 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL M 49 " --> pdb=" O MET M 18 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N MET M 18 " --> pdb=" O VAL M 49 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'O' and resid 3 through 8 removed outlier: 3.514A pdb=" N SER O 69 " --> pdb=" O CYS O 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS O 82 " --> pdb=" O VAL O 67 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL O 67 " --> pdb=" O HIS O 82 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY O 20 " --> pdb=" O TYR O 47 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL O 49 " --> pdb=" O MET O 18 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N MET O 18 " --> pdb=" O VAL O 49 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'P' and resid 3 through 8 removed outlier: 3.514A pdb=" N SER P 69 " --> pdb=" O CYS P 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS P 82 " --> pdb=" O VAL P 67 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL P 67 " --> pdb=" O HIS P 82 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'P' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY P 20 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL P 49 " --> pdb=" O MET P 18 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N MET P 18 " --> pdb=" O VAL P 49 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 3 through 8 removed outlier: 3.514A pdb=" N SER Q 69 " --> pdb=" O CYS Q 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS Q 82 " --> pdb=" O VAL Q 67 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL Q 67 " --> pdb=" O HIS Q 82 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY Q 20 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL Q 49 " --> pdb=" O MET Q 18 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N MET Q 18 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'R' and resid 3 through 8 removed outlier: 3.513A pdb=" N SER R 69 " --> pdb=" O CYS R 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS R 82 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL R 67 " --> pdb=" O HIS R 82 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'R' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY R 20 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL R 49 " --> pdb=" O MET R 18 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N MET R 18 " --> pdb=" O VAL R 49 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.513A pdb=" N SER S 69 " --> pdb=" O CYS S 80 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS S 82 " --> pdb=" O VAL S 67 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL S 67 " --> pdb=" O HIS S 82 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'S' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY S 20 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL S 49 " --> pdb=" O MET S 18 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N MET S 18 " --> pdb=" O VAL S 49 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'T' and resid 3 through 8 removed outlier: 3.513A pdb=" N SER T 69 " --> pdb=" O CYS T 80 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS T 82 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL T 67 " --> pdb=" O HIS T 82 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'T' and resid 35 through 37 removed outlier: 4.015A pdb=" N GLY T 20 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL T 49 " --> pdb=" O MET T 18 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N MET T 18 " --> pdb=" O VAL T 49 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 9.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6846 1.34 - 1.45: 3135 1.45 - 1.57: 11509 1.57 - 1.69: 50 1.69 - 1.81: 310 Bond restraints: 21850 Sorted by residual: bond pdb=" C1' 8GT I 301 " pdb=" C2' 8GT I 301 " ideal model delta sigma weight residual 1.268 1.520 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C1' 8GT E 301 " pdb=" C2' 8GT E 301 " ideal model delta sigma weight residual 1.268 1.520 -0.252 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C1' 8GT J 301 " pdb=" C2' 8GT J 301 " ideal model delta sigma weight residual 1.268 1.519 -0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C1' 8GT B 301 " pdb=" C2' 8GT B 301 " ideal model delta sigma weight residual 1.268 1.519 -0.251 2.00e-02 2.50e+03 1.58e+02 bond pdb=" C1' 8GT F 302 " pdb=" C2' 8GT F 302 " ideal model delta sigma weight residual 1.268 1.519 -0.251 2.00e-02 2.50e+03 1.58e+02 ... (remaining 21845 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.51: 600 105.51 - 112.64: 11306 112.64 - 119.76: 7449 119.76 - 126.88: 9883 126.88 - 134.01: 332 Bond angle restraints: 29570 Sorted by residual: angle pdb=" C GLN L 9 " pdb=" N ILE L 10 " pdb=" CA ILE L 10 " ideal model delta sigma weight residual 121.97 130.85 -8.88 1.80e+00 3.09e-01 2.43e+01 angle pdb=" C GLN O 9 " pdb=" N ILE O 10 " pdb=" CA ILE O 10 " ideal model delta sigma weight residual 121.97 130.84 -8.87 1.80e+00 3.09e-01 2.43e+01 angle pdb=" C GLN R 9 " pdb=" N ILE R 10 " pdb=" CA ILE R 10 " ideal model delta sigma weight residual 121.97 130.84 -8.87 1.80e+00 3.09e-01 2.43e+01 angle pdb=" C GLN N 9 " pdb=" N ILE N 10 " pdb=" CA ILE N 10 " ideal model delta sigma weight residual 121.97 130.83 -8.86 1.80e+00 3.09e-01 2.42e+01 angle pdb=" C GLN S 9 " pdb=" N ILE S 10 " pdb=" CA ILE S 10 " ideal model delta sigma weight residual 121.97 130.83 -8.86 1.80e+00 3.09e-01 2.42e+01 ... (remaining 29565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 12431 14.13 - 28.25: 519 28.25 - 42.38: 168 42.38 - 56.50: 52 56.50 - 70.63: 10 Dihedral angle restraints: 13180 sinusoidal: 5490 harmonic: 7690 Sorted by residual: dihedral pdb=" CA GLN O 9 " pdb=" C GLN O 9 " pdb=" N ILE O 10 " pdb=" CA ILE O 10 " ideal model delta harmonic sigma weight residual -180.00 -151.23 -28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLN L 9 " pdb=" C GLN L 9 " pdb=" N ILE L 10 " pdb=" CA ILE L 10 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLN Q 9 " pdb=" C GLN Q 9 " pdb=" N ILE Q 10 " pdb=" CA ILE Q 10 " ideal model delta harmonic sigma weight residual 180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 13177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2670 0.080 - 0.161: 611 0.161 - 0.241: 59 0.241 - 0.322: 0 0.322 - 0.402: 10 Chirality restraints: 3350 Sorted by residual: chirality pdb=" C2' 8GT D 302 " pdb=" C1' 8GT D 302 " pdb=" C3' 8GT D 302 " pdb=" O2' 8GT D 302 " both_signs ideal model delta sigma weight residual False -2.39 -2.79 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C2' 8GT F 301 " pdb=" C1' 8GT F 301 " pdb=" C3' 8GT F 301 " pdb=" O2' 8GT F 301 " both_signs ideal model delta sigma weight residual False -2.39 -2.79 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C2' 8GT J 301 " pdb=" C1' 8GT J 301 " pdb=" C3' 8GT J 301 " pdb=" O2' 8GT J 301 " both_signs ideal model delta sigma weight residual False -2.39 -2.79 0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 3347 not shown) Planarity restraints: 3710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 8GT B 301 " -0.059 2.00e-02 2.50e+03 2.84e-02 2.62e+01 pdb=" C2 8GT B 301 " 0.015 2.00e-02 2.50e+03 pdb=" C4 8GT B 301 " -0.014 2.00e-02 2.50e+03 pdb=" C5 8GT B 301 " -0.013 2.00e-02 2.50e+03 pdb=" C6 8GT B 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8 8GT B 301 " 0.018 2.00e-02 2.50e+03 pdb=" N1 8GT B 301 " 0.019 2.00e-02 2.50e+03 pdb=" N2 8GT B 301 " 0.032 2.00e-02 2.50e+03 pdb=" N3 8GT B 301 " -0.003 2.00e-02 2.50e+03 pdb=" N7 8GT B 301 " 0.006 2.00e-02 2.50e+03 pdb=" N9 8GT B 301 " -0.005 2.00e-02 2.50e+03 pdb=" O6 8GT B 301 " -0.042 2.00e-02 2.50e+03 pdb=" O8 8GT B 301 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 8GT D 301 " 0.059 2.00e-02 2.50e+03 2.84e-02 2.62e+01 pdb=" C2 8GT D 301 " -0.015 2.00e-02 2.50e+03 pdb=" C4 8GT D 301 " 0.014 2.00e-02 2.50e+03 pdb=" C5 8GT D 301 " 0.013 2.00e-02 2.50e+03 pdb=" C6 8GT D 301 " 0.007 2.00e-02 2.50e+03 pdb=" C8 8GT D 301 " -0.018 2.00e-02 2.50e+03 pdb=" N1 8GT D 301 " -0.018 2.00e-02 2.50e+03 pdb=" N2 8GT D 301 " -0.032 2.00e-02 2.50e+03 pdb=" N3 8GT D 301 " 0.004 2.00e-02 2.50e+03 pdb=" N7 8GT D 301 " -0.006 2.00e-02 2.50e+03 pdb=" N9 8GT D 301 " 0.005 2.00e-02 2.50e+03 pdb=" O6 8GT D 301 " 0.042 2.00e-02 2.50e+03 pdb=" O8 8GT D 301 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 8GT F 301 " 0.059 2.00e-02 2.50e+03 2.83e-02 2.61e+01 pdb=" C2 8GT F 301 " -0.015 2.00e-02 2.50e+03 pdb=" C4 8GT F 301 " 0.014 2.00e-02 2.50e+03 pdb=" C5 8GT F 301 " 0.013 2.00e-02 2.50e+03 pdb=" C6 8GT F 301 " 0.006 2.00e-02 2.50e+03 pdb=" C8 8GT F 301 " -0.018 2.00e-02 2.50e+03 pdb=" N1 8GT F 301 " -0.018 2.00e-02 2.50e+03 pdb=" N2 8GT F 301 " -0.032 2.00e-02 2.50e+03 pdb=" N3 8GT F 301 " 0.004 2.00e-02 2.50e+03 pdb=" N7 8GT F 301 " -0.006 2.00e-02 2.50e+03 pdb=" N9 8GT F 301 " 0.005 2.00e-02 2.50e+03 pdb=" O6 8GT F 301 " 0.042 2.00e-02 2.50e+03 pdb=" O8 8GT F 301 " -0.053 2.00e-02 2.50e+03 ... (remaining 3707 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 185 2.60 - 3.18: 15678 3.18 - 3.75: 30713 3.75 - 4.33: 46140 4.33 - 4.90: 80310 Nonbonded interactions: 173026 Sorted by model distance: nonbonded pdb=" O8 8GT E 301 " pdb="ZN ZN E 302 " model vdw 2.030 2.230 nonbonded pdb="ZN ZN H 302 " pdb=" O8 8GT I 301 " model vdw 2.131 2.230 nonbonded pdb=" O8 8GT F 301 " pdb="ZN ZN F 303 " model vdw 2.144 2.230 nonbonded pdb=" O8 8GT D 301 " pdb="ZN ZN D 303 " model vdw 2.151 2.230 nonbonded pdb="ZN ZN A 301 " pdb=" O8 8GT B 301 " model vdw 2.172 2.230 ... (remaining 173021 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 68 through 249) selection = (chain 'B' and resid 68 through 249) selection = (chain 'C' and resid 68 through 249) selection = (chain 'D' and resid 68 through 249) selection = (chain 'E' and resid 68 through 249) selection = (chain 'F' and resid 68 through 249) selection = (chain 'G' and resid 68 through 249) selection = (chain 'H' and resid 68 through 249) selection = (chain 'I' and resid 68 through 249) selection = (chain 'J' and resid 68 through 249) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 6 Type Number sf(0) Gaussians Zn 10 6.06 5 P 30 5.49 5 S 170 5.16 5 C 13520 2.51 5 N 3740 2.21 5 O 3990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.010 Extract box with map and model: 4.790 Check model and map are aligned: 0.310 Convert atoms to be neutral: 0.170 Process input model: 59.060 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 0.016 0.252 21850 Z= 0.995 Angle : 1.216 9.874 29570 Z= 0.656 Chirality : 0.068 0.402 3350 Planarity : 0.007 0.047 3710 Dihedral : 9.980 70.627 8200 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.45 % Favored : 96.17 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.14), residues: 2610 helix: -4.48 (0.08), residues: 890 sheet: 0.34 (0.21), residues: 670 loop : -2.27 (0.16), residues: 1050 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 635 time to evaluate : 2.489 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 635 average time/residue: 1.4063 time to fit residues: 1001.9985 Evaluate side-chains 489 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 2.476 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 188 GLN L 31 HIS ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 188 GLN C 126 HIS E 126 HIS G 126 HIS G 188 GLN H 126 HIS I 126 HIS I 188 GLN J 126 HIS J 180 GLN J 188 GLN F 126 HIS D 126 HIS D 188 GLN K 31 HIS ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 31 HIS O 82 HIS P 31 HIS ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS Q 82 HIS R 31 HIS S 31 HIS ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 21850 Z= 0.198 Angle : 0.651 6.811 29570 Z= 0.345 Chirality : 0.049 0.165 3350 Planarity : 0.005 0.066 3710 Dihedral : 6.457 46.670 2920 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer Outliers : 4.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.14), residues: 2610 helix: -3.02 (0.12), residues: 980 sheet: 0.08 (0.21), residues: 650 loop : -1.79 (0.16), residues: 980 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 481 time to evaluate : 2.720 Fit side-chains revert: symmetry clash outliers start: 98 outliers final: 46 residues processed: 514 average time/residue: 1.3440 time to fit residues: 784.1878 Evaluate side-chains 464 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 418 time to evaluate : 2.540 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 22 residues processed: 24 average time/residue: 0.7753 time to fit residues: 26.2935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 196 optimal weight: 0.0870 chunk 160 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 80 optimal weight: 0.0470 chunk 189 optimal weight: 0.0970 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN E 222 ASN G 188 GLN I 188 GLN J 188 GLN D 188 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 HIS ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 ASN ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 21850 Z= 0.136 Angle : 0.544 5.906 29570 Z= 0.288 Chirality : 0.046 0.140 3350 Planarity : 0.004 0.040 3710 Dihedral : 5.891 45.189 2920 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.15), residues: 2610 helix: -1.66 (0.15), residues: 980 sheet: 0.10 (0.20), residues: 710 loop : -1.31 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 425 time to evaluate : 2.752 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 34 residues processed: 454 average time/residue: 1.3055 time to fit residues: 674.1166 Evaluate side-chains 425 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 391 time to evaluate : 2.616 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 26 residues processed: 9 average time/residue: 0.7321 time to fit residues: 11.4386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 0.0170 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 237 optimal weight: 6.9990 chunk 251 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 224 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN L 42 ASN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 188 GLN E 188 GLN G 188 GLN H 188 GLN I 188 GLN J 188 GLN F 188 GLN D 188 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 HIS ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 HIS ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 21850 Z= 0.146 Angle : 0.540 6.672 29570 Z= 0.282 Chirality : 0.046 0.140 3350 Planarity : 0.004 0.042 3710 Dihedral : 5.620 45.679 2920 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.16), residues: 2610 helix: -0.91 (0.17), residues: 980 sheet: 0.29 (0.21), residues: 710 loop : -1.19 (0.18), residues: 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 405 time to evaluate : 2.754 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 40 residues processed: 441 average time/residue: 1.2732 time to fit residues: 639.8763 Evaluate side-chains 426 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 386 time to evaluate : 2.390 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 26 residues processed: 16 average time/residue: 0.5497 time to fit residues: 15.2079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 188 GLN E 188 GLN G 188 GLN H 188 GLN I 188 GLN J 188 GLN F 188 GLN D 188 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 HIS ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 21850 Z= 0.189 Angle : 0.565 8.455 29570 Z= 0.294 Chirality : 0.047 0.148 3350 Planarity : 0.004 0.038 3710 Dihedral : 5.498 45.459 2920 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 3.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2610 helix: -0.50 (0.17), residues: 990 sheet: 0.34 (0.20), residues: 710 loop : -1.14 (0.19), residues: 910 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 403 time to evaluate : 2.562 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 52 residues processed: 439 average time/residue: 1.3289 time to fit residues: 659.5404 Evaluate side-chains 435 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 383 time to evaluate : 2.511 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 31 residues processed: 22 average time/residue: 0.4807 time to fit residues: 17.5539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 6.9990 chunk 226 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 251 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 ASN ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN B 188 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN G 180 GLN ** G 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 188 GLN I 118 ASN I 188 GLN J 188 GLN F 118 ASN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN D 188 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 HIS ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.073 21850 Z= 0.504 Angle : 0.819 11.050 29570 Z= 0.415 Chirality : 0.058 0.174 3350 Planarity : 0.007 0.057 3710 Dihedral : 6.102 49.944 2920 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.56 % Favored : 94.41 % Rotamer Outliers : 4.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.16), residues: 2610 helix: -0.78 (0.16), residues: 980 sheet: 0.17 (0.19), residues: 760 loop : -1.47 (0.19), residues: 870 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 432 time to evaluate : 2.778 Fit side-chains outliers start: 108 outliers final: 61 residues processed: 482 average time/residue: 1.2401 time to fit residues: 683.4789 Evaluate side-chains 469 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 408 time to evaluate : 2.457 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 35 residues processed: 26 average time/residue: 0.8730 time to fit residues: 30.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 211 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 188 GLN J 188 GLN F 110 GLN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 21850 Z= 0.170 Angle : 0.577 7.733 29570 Z= 0.302 Chirality : 0.047 0.166 3350 Planarity : 0.004 0.042 3710 Dihedral : 5.764 46.274 2920 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2610 helix: -0.42 (0.17), residues: 980 sheet: 0.26 (0.20), residues: 710 loop : -1.12 (0.19), residues: 920 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 399 time to evaluate : 2.628 Fit side-chains outliers start: 79 outliers final: 49 residues processed: 439 average time/residue: 1.2788 time to fit residues: 640.2033 Evaluate side-chains 437 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 388 time to evaluate : 2.819 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 34 residues processed: 16 average time/residue: 0.7577 time to fit residues: 18.7328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 196 optimal weight: 0.0980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 188 GLN E 188 GLN G 188 GLN H 188 GLN I 188 GLN J 188 GLN F 188 GLN D 188 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 21850 Z= 0.280 Angle : 0.642 8.120 29570 Z= 0.332 Chirality : 0.050 0.177 3350 Planarity : 0.005 0.038 3710 Dihedral : 5.780 47.739 2920 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2610 helix: -0.45 (0.17), residues: 980 sheet: 0.29 (0.20), residues: 710 loop : -0.98 (0.20), residues: 920 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 402 time to evaluate : 2.505 Fit side-chains outliers start: 93 outliers final: 60 residues processed: 439 average time/residue: 1.2986 time to fit residues: 648.4285 Evaluate side-chains 457 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 397 time to evaluate : 2.524 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 36 residues processed: 25 average time/residue: 0.8851 time to fit residues: 30.0178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.9990 chunk 240 optimal weight: 7.9990 chunk 219 optimal weight: 0.5980 chunk 233 optimal weight: 0.0870 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 211 optimal weight: 0.9990 chunk 220 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 75 GLN B 188 GLN C 188 GLN E 188 GLN H 188 GLN I 188 GLN J 188 GLN F 188 GLN D 188 GLN K 75 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 42 ASN ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 HIS T 75 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 21850 Z= 0.150 Angle : 0.547 6.236 29570 Z= 0.288 Chirality : 0.046 0.172 3350 Planarity : 0.004 0.037 3710 Dihedral : 5.567 45.397 2920 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.17), residues: 2610 helix: -0.21 (0.18), residues: 990 sheet: 0.65 (0.22), residues: 650 loop : -1.09 (0.19), residues: 970 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 396 time to evaluate : 2.497 Fit side-chains outliers start: 57 outliers final: 41 residues processed: 430 average time/residue: 1.2949 time to fit residues: 632.9832 Evaluate side-chains 429 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 388 time to evaluate : 2.503 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 32 residues processed: 9 average time/residue: 0.8558 time to fit residues: 12.7405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.1980 chunk 246 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 171 optimal weight: 7.9990 chunk 259 optimal weight: 0.7980 chunk 238 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 126 optimal weight: 0.0570 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN B 188 GLN C 188 GLN E 188 GLN G 188 GLN H 188 GLN I 188 GLN J 188 GLN F 110 GLN F 188 GLN D 188 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 21850 Z= 0.197 Angle : 0.582 6.712 29570 Z= 0.304 Chirality : 0.048 0.188 3350 Planarity : 0.004 0.036 3710 Dihedral : 5.542 46.654 2920 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.17), residues: 2610 helix: -0.17 (0.17), residues: 990 sheet: 0.57 (0.21), residues: 710 loop : -0.88 (0.20), residues: 910 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 394 time to evaluate : 2.575 Fit side-chains outliers start: 57 outliers final: 41 residues processed: 427 average time/residue: 1.3217 time to fit residues: 640.7472 Evaluate side-chains 431 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 390 time to evaluate : 2.520 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 33 residues processed: 10 average time/residue: 0.9905 time to fit residues: 15.0319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 3.9990 chunk 219 optimal weight: 0.4980 chunk 63 optimal weight: 0.0980 chunk 190 optimal weight: 7.9990 chunk 30 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN L 42 ASN B 188 GLN C 188 GLN E 188 GLN G 118 ASN G 188 GLN H 188 GLN I 188 GLN J 188 GLN F 188 GLN D 118 ASN D 188 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 42 ASN ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.215819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.192882 restraints weight = 21783.650| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 1.66 r_work: 0.4210 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 1.50 restraints_weight: 0.2500 r_work: 0.4181 rms_B_bonded: 1.63 restraints_weight: 0.1250 r_work: 0.4163 rms_B_bonded: 1.84 restraints_weight: 0.0625 r_work: 0.4143 rms_B_bonded: 2.12 restraints_weight: 0.0312 r_work: 0.4120 rms_B_bonded: 2.50 restraints_weight: 0.0156 r_work: 0.4092 rms_B_bonded: 2.97 restraints_weight: 0.0078 r_work: 0.4060 rms_B_bonded: 3.57 restraints_weight: 0.0039 r_work: 0.4020 rms_B_bonded: 4.34 restraints_weight: 0.0020 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 21850 Z= 0.138 Angle : 0.544 14.220 29570 Z= 0.284 Chirality : 0.045 0.172 3350 Planarity : 0.003 0.035 3710 Dihedral : 5.388 45.077 2920 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2610 helix: 0.03 (0.18), residues: 990 sheet: 0.84 (0.22), residues: 650 loop : -0.88 (0.19), residues: 970 =============================================================================== Job complete usr+sys time: 9173.61 seconds wall clock time: 162 minutes 47.28 seconds (9767.28 seconds total)