Starting phenix.real_space_refine on Sat Feb 24 07:42:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/02_2024/6z80_11113_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/02_2024/6z80_11113.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/02_2024/6z80_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_11113/02_2024/6z80_11113_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/02_2024/6z80_11113_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/02_2024/6z80_11113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/02_2024/6z80_11113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/02_2024/6z80_11113_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z80_11113/02_2024/6z80_11113_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 21340 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Process input model Symmetric amino acids flipped Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 62": "NH1" <-> "NH2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 216": "NH1" <-> "NH2" Residue "C ARG 235": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 249": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 216": "NH1" <-> "NH2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ARG 249": "NH1" <-> "NH2" Residue "H ARG 88": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 235": "NH1" <-> "NH2" Residue "H ARG 249": "NH1" <-> "NH2" Residue "I ARG 88": "NH1" <-> "NH2" Residue "I ARG 216": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "J ARG 88": "NH1" <-> "NH2" Residue "J ARG 216": "NH1" <-> "NH2" Residue "J ARG 235": "NH1" <-> "NH2" Residue "J ARG 249": "NH1" <-> "NH2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 216": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 249": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 62": "NH1" <-> "NH2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 62": "NH1" <-> "NH2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 38": "NH1" <-> "NH2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 62": "NH1" <-> "NH2" Residue "T PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} 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: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "N" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "M" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "O" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "P" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "Q" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "R" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "S" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} Chain: "T" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 669 Classifications: {'peptide': 83} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 77} 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: {' ZN': 1, '8GT': 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: {' ZN': 1, '8GT': 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: {' ZN': 1, '8GT': 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: {' ZN': 1, '8GT': 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: {' ZN': 1, '8GT': 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: {' ZN': 1, '8GT': 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: {' ZN': 1, '8GT': 2} 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: {' ZN': 1, '8GT': 2} 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: 10.90, per 1000 atoms: 0.51 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: 7.80 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal 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: 4.14 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: 7.43 Time building geometry restraints manager: 8.39 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=" C2' 8GT D 302 " pdb=" C3' 8GT D 302 " ideal model delta sigma weight residual 1.237 1.538 -0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C2' 8GT F 301 " pdb=" C3' 8GT F 301 " ideal model delta sigma weight residual 1.237 1.538 -0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C2' 8GT C 301 " pdb=" C3' 8GT C 301 " ideal model delta sigma weight residual 1.237 1.538 -0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C2' 8GT H 301 " pdb=" C3' 8GT H 301 " ideal model delta sigma weight residual 1.237 1.538 -0.301 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C2' 8GT D 301 " pdb=" C3' 8GT D 301 " ideal model delta sigma weight residual 1.237 1.537 -0.300 2.00e-02 2.50e+03 2.26e+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: 12451 14.13 - 28.25: 529 28.25 - 42.38: 188 42.38 - 56.50: 52 56.50 - 70.63: 20 Dihedral angle restraints: 13240 sinusoidal: 5550 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 13237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2669 0.083 - 0.165: 617 0.165 - 0.248: 44 0.248 - 0.331: 10 0.331 - 0.414: 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 -2.38 -2.79 0.41 2.00e-01 2.50e+01 4.28e+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 -2.38 -2.79 0.41 2.00e-01 2.50e+01 4.25e+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 -2.38 -2.79 0.41 2.00e-01 2.50e+01 4.22e+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 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: 0.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.020 Extract box with map and model: 4.100 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 60.510 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.015 0.301 21850 Z= 0.981 Angle : 1.215 10.034 29570 Z= 0.656 Chirality : 0.070 0.414 3350 Planarity : 0.007 0.047 3710 Dihedral : 10.236 70.627 8260 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 % Allowed : 1.28 % Favored : 98.72 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 96 HIS 0.010 0.002 HIS J 210 PHE 0.035 0.005 PHE A 234 TYR 0.031 0.004 TYR I 75 ARG 0.009 0.001 ARG B 235 *********************** 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 : 2.595 Fit side-chains REVERT: A 93 LYS cc_start: 0.7666 (mttm) cc_final: 0.6762 (tttm) REVERT: A 175 TYR cc_start: 0.8427 (m-80) cc_final: 0.8151 (m-80) REVERT: A 238 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.7987 (Cg_exo) REVERT: B 93 LYS cc_start: 0.7471 (mttm) cc_final: 0.6406 (tttm) REVERT: B 175 TYR cc_start: 0.8468 (m-80) cc_final: 0.8236 (m-80) REVERT: B 213 MET cc_start: 0.7943 (mtp) cc_final: 0.7689 (mtm) REVERT: C 175 TYR cc_start: 0.8273 (m-80) cc_final: 0.7981 (m-80) REVERT: C 241 ARG cc_start: 0.7734 (ttp-110) cc_final: 0.7497 (ttm170) REVERT: C 246 THR cc_start: 0.8581 (m) cc_final: 0.8218 (p) REVERT: E 175 TYR cc_start: 0.8405 (m-80) cc_final: 0.8175 (m-80) REVERT: E 213 MET cc_start: 0.7877 (mtp) cc_final: 0.7547 (mtm) REVERT: E 241 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7424 (ttm110) REVERT: G 93 LYS cc_start: 0.7574 (mttm) cc_final: 0.6841 (tttm) REVERT: G 175 TYR cc_start: 0.8384 (m-80) cc_final: 0.8056 (m-80) REVERT: H 173 GLU cc_start: 0.5589 (tp30) cc_final: 0.5326 (tp30) REVERT: H 213 MET cc_start: 0.7857 (mtp) cc_final: 0.7468 (mtm) REVERT: I 93 LYS cc_start: 0.7578 (mttm) cc_final: 0.6730 (tttm) REVERT: I 140 MET cc_start: 0.7124 (mmm) cc_final: 0.6765 (mmm) REVERT: I 175 TYR cc_start: 0.8443 (m-80) cc_final: 0.8192 (m-80) REVERT: J 93 LYS cc_start: 0.7505 (mttm) cc_final: 0.6627 (tttm) REVERT: J 175 TYR cc_start: 0.8434 (m-80) cc_final: 0.8193 (m-80) REVERT: J 213 MET cc_start: 0.8016 (mtp) cc_final: 0.7740 (mtm) REVERT: F 175 TYR cc_start: 0.8108 (m-80) cc_final: 0.7781 (m-80) REVERT: F 213 MET cc_start: 0.7963 (mtp) cc_final: 0.7718 (mtp) REVERT: F 246 THR cc_start: 0.8339 (m) cc_final: 0.7844 (p) REVERT: D 175 TYR cc_start: 0.8192 (m-80) cc_final: 0.7783 (m-80) REVERT: N 12 MET cc_start: 0.6400 (ptt) cc_final: 0.6017 (ptt) REVERT: T 13 GLU cc_start: 0.7018 (mp0) cc_final: 0.6694 (mp0) outliers start: 0 outliers final: 0 residues processed: 635 average time/residue: 1.5294 time to fit residues: 1081.9810 Evaluate side-chains 496 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.353 ------------------------------------------------------------------------------- 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: 0.8980 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: 5.9990 chunk 203 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 236 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 188 GLN L 31 HIS B 126 HIS B 188 GLN C 126 HIS E 126 HIS G 126 HIS G 188 GLN H 126 HIS I 126 HIS 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: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21850 Z= 0.176 Angle : 0.634 6.509 29570 Z= 0.334 Chirality : 0.049 0.170 3350 Planarity : 0.005 0.037 3710 Dihedral : 7.480 59.887 2980 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 4.02 % Allowed : 9.19 % Favored : 86.79 % 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: -2.80 (0.14), residues: 2610 helix: -2.99 (0.12), residues: 980 sheet: 0.07 (0.21), residues: 650 loop : -1.76 (0.16), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 79 HIS 0.011 0.001 HIS N 31 PHE 0.017 0.002 PHE F 148 TYR 0.012 0.001 TYR G 156 ARG 0.006 0.001 ARG R 62 *********************** 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 571 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 477 time to evaluate : 2.367 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7544 (mttm) cc_final: 0.6688 (tttm) REVERT: A 242 GLU cc_start: 0.7117 (tp30) cc_final: 0.6765 (tp30) REVERT: B 93 LYS cc_start: 0.7300 (mttm) cc_final: 0.6319 (tttm) REVERT: C 70 ASN cc_start: 0.6522 (OUTLIER) cc_final: 0.6274 (t0) REVERT: C 219 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6800 (mt0) REVERT: E 213 MET cc_start: 0.7846 (mtp) cc_final: 0.7553 (mtm) REVERT: E 219 GLN cc_start: 0.7442 (mt0) cc_final: 0.7081 (mt0) REVERT: E 239 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7325 (mmmt) REVERT: G 93 LYS cc_start: 0.7629 (mttm) cc_final: 0.6782 (tttm) REVERT: G 219 GLN cc_start: 0.7195 (mt0) cc_final: 0.6706 (mt0) REVERT: H 133 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7930 (pttp) REVERT: H 173 GLU cc_start: 0.5167 (tp30) cc_final: 0.4914 (tp30) REVERT: H 213 MET cc_start: 0.7908 (mtp) cc_final: 0.7560 (mtm) REVERT: H 239 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7299 (mmmt) REVERT: I 93 LYS cc_start: 0.7522 (mttm) cc_final: 0.6745 (tttm) REVERT: J 93 LYS cc_start: 0.7283 (mttm) cc_final: 0.6479 (tttm) REVERT: J 213 MET cc_start: 0.7988 (mtp) cc_final: 0.7785 (mtm) REVERT: J 219 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: F 219 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6913 (mt0) REVERT: F 239 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7132 (mmmt) REVERT: D 102 MET cc_start: 0.4814 (tpt) cc_final: 0.4255 (tpt) REVERT: D 118 ASN cc_start: 0.7165 (t0) cc_final: 0.6614 (t0) REVERT: D 219 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6659 (mt0) REVERT: N 12 MET cc_start: 0.6361 (ptt) cc_final: 0.5897 (ptt) outliers start: 94 outliers final: 35 residues processed: 509 average time/residue: 1.3931 time to fit residues: 798.2196 Evaluate side-chains 456 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 412 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 133 LYS Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 18 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 255 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 222 ASN G 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21850 Z= 0.268 Angle : 0.653 6.534 29570 Z= 0.338 Chirality : 0.051 0.191 3350 Planarity : 0.005 0.041 3710 Dihedral : 7.091 59.359 2980 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 4.53 % Allowed : 12.35 % Favored : 83.12 % 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: -1.93 (0.15), residues: 2610 helix: -1.72 (0.15), residues: 990 sheet: 0.05 (0.20), residues: 710 loop : -1.64 (0.17), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Q 79 HIS 0.008 0.001 HIS N 31 PHE 0.017 0.002 PHE J 148 TYR 0.014 0.002 TYR G 156 ARG 0.008 0.001 ARG R 66 *********************** 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 530 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 424 time to evaluate : 2.351 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7586 (mttm) cc_final: 0.6730 (tttm) REVERT: A 216 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7538 (ptm160) REVERT: B 93 LYS cc_start: 0.7434 (mttm) cc_final: 0.6384 (tttm) REVERT: B 137 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6912 (ppp) REVERT: B 216 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.6650 (ptm160) REVERT: B 219 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6600 (mt0) REVERT: C 216 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6447 (ptm160) REVERT: C 219 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6832 (mt0) REVERT: C 239 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7555 (mmmt) REVERT: E 213 MET cc_start: 0.7991 (mtp) cc_final: 0.7657 (mtm) REVERT: E 216 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7078 (ptm160) REVERT: E 219 GLN cc_start: 0.7370 (mt0) cc_final: 0.7007 (mt0) REVERT: E 239 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7257 (mmmt) REVERT: G 93 LYS cc_start: 0.7653 (mttm) cc_final: 0.6778 (tttm) REVERT: G 173 GLU cc_start: 0.5658 (OUTLIER) cc_final: 0.5066 (mm-30) REVERT: G 216 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7312 (ptm160) REVERT: H 213 MET cc_start: 0.8008 (mtp) cc_final: 0.7665 (mtp) REVERT: H 216 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7232 (ptm-80) REVERT: H 239 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7085 (mmmt) REVERT: I 93 LYS cc_start: 0.7539 (mttm) cc_final: 0.6733 (tttm) REVERT: I 118 ASN cc_start: 0.6994 (t0) cc_final: 0.6668 (t0) REVERT: I 219 GLN cc_start: 0.7382 (OUTLIER) cc_final: 0.6866 (mt0) REVERT: J 93 LYS cc_start: 0.7454 (mttm) cc_final: 0.6636 (tttm) REVERT: J 137 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6868 (ppp) REVERT: J 219 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6437 (mt0) REVERT: F 102 MET cc_start: 0.4496 (tpt) cc_final: 0.4291 (tpt) REVERT: F 133 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7861 (ptmm) REVERT: F 216 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6387 (ptm160) REVERT: F 239 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7450 (mmmt) REVERT: D 102 MET cc_start: 0.4674 (tpt) cc_final: 0.4310 (tpt) REVERT: D 216 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7508 (ptm160) REVERT: D 219 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6708 (mt0) REVERT: N 12 MET cc_start: 0.6316 (ptt) cc_final: 0.5890 (ptt) REVERT: S 62 ARG cc_start: 0.7276 (mtm110) cc_final: 0.7047 (mtp180) REVERT: T 22 GLU cc_start: 0.7511 (pm20) cc_final: 0.7238 (pm20) outliers start: 106 outliers final: 53 residues processed: 461 average time/residue: 1.4091 time to fit residues: 731.0805 Evaluate side-chains 475 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 401 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 187 LYS Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 216 ARG Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 239 LYS Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 18 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 237 optimal weight: 8.9990 chunk 251 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 180 GLN B 188 GLN C 188 GLN G 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 42 ASN ** 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: 0.7044 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21850 Z= 0.211 Angle : 0.593 7.551 29570 Z= 0.308 Chirality : 0.048 0.149 3350 Planarity : 0.004 0.039 3710 Dihedral : 6.927 59.844 2980 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.44 % Allowed : 14.66 % Favored : 80.90 % 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: -1.35 (0.16), residues: 2610 helix: -1.02 (0.16), residues: 990 sheet: 0.17 (0.20), residues: 710 loop : -1.41 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 79 HIS 0.005 0.001 HIS N 31 PHE 0.017 0.002 PHE G 148 TYR 0.018 0.002 TYR G 75 ARG 0.008 0.001 ARG S 66 *********************** 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 515 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 411 time to evaluate : 2.411 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7581 (mttm) cc_final: 0.6716 (tttm) REVERT: A 216 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7521 (ptm160) REVERT: B 93 LYS cc_start: 0.7515 (mttm) cc_final: 0.6466 (tttm) REVERT: B 137 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6867 (ppp) REVERT: B 216 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6626 (ptm160) REVERT: B 219 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6533 (mt0) REVERT: C 102 MET cc_start: 0.4542 (tpt) cc_final: 0.4256 (tpt) REVERT: C 216 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6598 (ptm160) REVERT: C 219 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6723 (mt0) REVERT: C 239 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7455 (mmmt) REVERT: E 213 MET cc_start: 0.7965 (mtp) cc_final: 0.7661 (mtm) REVERT: E 216 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7073 (ptm160) REVERT: E 219 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6937 (mt0) REVERT: G 93 LYS cc_start: 0.7631 (mttm) cc_final: 0.6744 (tttm) REVERT: G 102 MET cc_start: 0.4675 (tpt) cc_final: 0.4243 (tpt) REVERT: G 173 GLU cc_start: 0.5580 (OUTLIER) cc_final: 0.5016 (mm-30) REVERT: G 216 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7261 (ptm160) REVERT: G 219 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6521 (mt0) REVERT: H 213 MET cc_start: 0.8019 (mtp) cc_final: 0.7637 (mtm) REVERT: H 216 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7260 (ptm-80) REVERT: I 93 LYS cc_start: 0.7529 (mttm) cc_final: 0.6733 (tttm) REVERT: I 102 MET cc_start: 0.4503 (tpt) cc_final: 0.4165 (tpt) REVERT: I 118 ASN cc_start: 0.6998 (t0) cc_final: 0.6686 (t0) REVERT: I 219 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6830 (mt0) REVERT: J 93 LYS cc_start: 0.7420 (mttm) cc_final: 0.6635 (tttm) REVERT: J 137 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6896 (ppp) REVERT: J 219 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6492 (mt0) REVERT: F 137 MET cc_start: 0.7391 (tmm) cc_final: 0.7161 (tmm) REVERT: F 216 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6586 (ptm160) REVERT: F 219 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6762 (mt0) REVERT: F 239 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7121 (mmmt) REVERT: D 102 MET cc_start: 0.4867 (tpt) cc_final: 0.4638 (tpt) REVERT: D 173 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.5008 (mm-30) REVERT: D 216 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7365 (ptm160) REVERT: D 219 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6579 (mt0) REVERT: N 12 MET cc_start: 0.6364 (ptt) cc_final: 0.5925 (ptt) outliers start: 104 outliers final: 50 residues processed: 447 average time/residue: 1.4095 time to fit residues: 709.8539 Evaluate side-chains 465 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 393 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 216 ARG Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.0470 chunk 142 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 225 optimal weight: 0.2980 chunk 63 optimal weight: 9.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- 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 ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** O 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** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3217 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= 0.183 Angle : 0.570 6.500 29570 Z= 0.296 Chirality : 0.047 0.145 3350 Planarity : 0.004 0.039 3710 Dihedral : 6.729 59.978 2980 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.49 % Allowed : 15.94 % Favored : 79.57 % 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: -0.97 (0.16), residues: 2610 helix: -0.59 (0.17), residues: 990 sheet: 0.24 (0.20), residues: 710 loop : -1.23 (0.18), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 79 HIS 0.006 0.001 HIS R 31 PHE 0.016 0.002 PHE G 148 TYR 0.014 0.001 TYR E 175 ARG 0.009 0.000 ARG S 66 *********************** 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 502 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 397 time to evaluate : 2.460 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7585 (mttm) cc_final: 0.6724 (tttm) REVERT: A 216 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7496 (ptm160) REVERT: B 93 LYS cc_start: 0.7510 (mttm) cc_final: 0.6668 (tttm) REVERT: B 137 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6864 (ppp) REVERT: B 216 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.6902 (ptm160) REVERT: B 219 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6501 (mt0) REVERT: C 102 MET cc_start: 0.4504 (tpt) cc_final: 0.4241 (tpt) REVERT: C 216 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6725 (ptm160) REVERT: C 219 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6617 (mt0) REVERT: C 239 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7408 (mmmt) REVERT: E 93 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7640 (mttt) REVERT: E 102 MET cc_start: 0.4695 (OUTLIER) cc_final: 0.3899 (tpt) REVERT: E 140 MET cc_start: 0.7454 (tpt) cc_final: 0.7252 (mmp) REVERT: E 213 MET cc_start: 0.8036 (mtp) cc_final: 0.7760 (mtm) REVERT: E 216 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7065 (ptm160) REVERT: E 219 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6955 (mt0) REVERT: G 93 LYS cc_start: 0.7585 (mttm) cc_final: 0.6669 (tttm) REVERT: G 102 MET cc_start: 0.4565 (tpt) cc_final: 0.4300 (tpt) REVERT: G 173 GLU cc_start: 0.5594 (OUTLIER) cc_final: 0.4976 (mm-30) REVERT: G 216 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7257 (ptm160) REVERT: G 219 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6491 (mt0) REVERT: H 213 MET cc_start: 0.8076 (mtp) cc_final: 0.7748 (mtm) REVERT: I 93 LYS cc_start: 0.7535 (mttm) cc_final: 0.6746 (tttm) REVERT: I 102 MET cc_start: 0.4254 (tpt) cc_final: 0.4041 (tpp) REVERT: I 118 ASN cc_start: 0.6963 (t0) cc_final: 0.6696 (t0) REVERT: I 219 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6917 (mt0) REVERT: J 93 LYS cc_start: 0.7403 (mttm) cc_final: 0.6623 (tttm) REVERT: J 137 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6918 (ppp) REVERT: J 216 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7045 (ptm160) REVERT: J 219 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.6455 (mt0) REVERT: F 197 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6943 (mt) REVERT: F 216 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6707 (ptm160) REVERT: F 219 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6725 (mt0) REVERT: F 239 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7093 (mmmt) REVERT: D 102 MET cc_start: 0.4704 (tpt) cc_final: 0.4500 (tpt) REVERT: D 173 GLU cc_start: 0.5657 (OUTLIER) cc_final: 0.4997 (mm-30) REVERT: D 216 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7389 (ptm160) REVERT: D 219 GLN cc_start: 0.7127 (OUTLIER) cc_final: 0.6589 (mt0) REVERT: K 1 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5517 (ptt) REVERT: N 12 MET cc_start: 0.6362 (ptt) cc_final: 0.5887 (ptt) REVERT: S 1 MET cc_start: 0.5796 (OUTLIER) cc_final: 0.5469 (ptt) outliers start: 105 outliers final: 55 residues processed: 438 average time/residue: 1.3536 time to fit residues: 669.6415 Evaluate side-chains 464 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 382 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 251 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 180 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN H 188 GLN I 188 GLN J 188 GLN F 118 ASN ** F 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 21850 Z= 0.332 Angle : 0.683 8.959 29570 Z= 0.348 Chirality : 0.052 0.207 3350 Planarity : 0.005 0.042 3710 Dihedral : 6.902 59.984 2980 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 5.04 % Allowed : 15.64 % Favored : 79.32 % 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: -0.99 (0.16), residues: 2610 helix: -0.52 (0.17), residues: 980 sheet: 0.15 (0.20), residues: 710 loop : -1.29 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 79 HIS 0.006 0.001 HIS F 144 PHE 0.019 0.002 PHE I 148 TYR 0.016 0.002 TYR E 175 ARG 0.009 0.001 ARG S 66 *********************** 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 527 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 409 time to evaluate : 2.218 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7507 (mttm) cc_final: 0.6740 (tttm) REVERT: A 102 MET cc_start: 0.5026 (OUTLIER) cc_final: 0.4361 (tpp) REVERT: A 118 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.6592 (t0) REVERT: A 216 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7521 (ptm160) REVERT: L 36 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7437 (tmtp) REVERT: B 93 LYS cc_start: 0.7485 (mttm) cc_final: 0.6633 (tttm) REVERT: B 137 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6967 (ppp) REVERT: B 216 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7019 (ptm160) REVERT: B 219 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6608 (mt0) REVERT: C 102 MET cc_start: 0.4533 (tpt) cc_final: 0.4225 (tpt) REVERT: C 216 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6760 (ptm160) REVERT: C 219 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6700 (mt0) REVERT: C 239 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7406 (mmmt) REVERT: E 93 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7672 (mttt) REVERT: E 102 MET cc_start: 0.4789 (OUTLIER) cc_final: 0.4085 (tpt) REVERT: E 213 MET cc_start: 0.8076 (mtp) cc_final: 0.7776 (mtm) REVERT: E 216 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7035 (ptm160) REVERT: E 219 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7022 (mt0) REVERT: E 239 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7115 (mmmt) REVERT: G 102 MET cc_start: 0.4613 (tpt) cc_final: 0.4357 (tpt) REVERT: G 173 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5041 (mm-30) REVERT: G 216 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7287 (ptm160) REVERT: G 219 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.6591 (mt0) REVERT: H 213 MET cc_start: 0.8055 (mtp) cc_final: 0.7752 (mtp) REVERT: H 216 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7269 (ptm-80) REVERT: I 93 LYS cc_start: 0.7568 (mttm) cc_final: 0.6739 (tttm) REVERT: I 118 ASN cc_start: 0.7009 (t0) cc_final: 0.6797 (t0) REVERT: I 219 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6833 (mt0) REVERT: I 239 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7619 (mmmt) REVERT: J 137 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6972 (ppp) REVERT: J 216 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.6991 (ptm160) REVERT: J 219 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6526 (mt0) REVERT: F 102 MET cc_start: 0.4551 (tpt) cc_final: 0.4313 (tpt) REVERT: F 216 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6738 (ptm160) REVERT: F 219 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6762 (mt0) REVERT: F 239 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7426 (mmmt) REVERT: D 173 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.4930 (mm-30) REVERT: D 216 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7382 (ptm160) REVERT: D 219 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6688 (mt0) REVERT: D 239 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7103 (mmpt) REVERT: K 1 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5626 (ptt) REVERT: N 12 MET cc_start: 0.6299 (ptt) cc_final: 0.5840 (ptt) REVERT: S 1 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5535 (ptt) outliers start: 118 outliers final: 61 residues processed: 452 average time/residue: 1.4415 time to fit residues: 739.4535 Evaluate side-chains 492 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 398 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 216 ARG Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 18 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 18 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 143 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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: 0.7058 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21850 Z= 0.199 Angle : 0.588 7.946 29570 Z= 0.304 Chirality : 0.048 0.151 3350 Planarity : 0.004 0.039 3710 Dihedral : 6.697 58.801 2980 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.62 % Allowed : 16.71 % Favored : 78.68 % 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: -0.79 (0.16), residues: 2610 helix: -0.36 (0.17), residues: 990 sheet: 0.27 (0.20), residues: 710 loop : -1.19 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 79 HIS 0.002 0.001 HIS C 144 PHE 0.018 0.002 PHE H 148 TYR 0.015 0.001 TYR E 175 ARG 0.008 0.000 ARG S 66 *********************** 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 511 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 403 time to evaluate : 2.364 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7431 (mttm) cc_final: 0.6664 (tttm) REVERT: A 102 MET cc_start: 0.4622 (tpt) cc_final: 0.4318 (tpt) REVERT: A 137 MET cc_start: 0.7444 (tmm) cc_final: 0.7217 (tmm) REVERT: A 216 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7485 (ptm160) REVERT: L 36 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7345 (tmtp) REVERT: B 93 LYS cc_start: 0.7550 (mttm) cc_final: 0.6633 (tttm) REVERT: B 137 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6919 (ppp) REVERT: B 216 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.6960 (ptm160) REVERT: B 219 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6504 (mt0) REVERT: C 102 MET cc_start: 0.4541 (tpt) cc_final: 0.4283 (tpt) REVERT: C 216 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6835 (ptm160) REVERT: C 219 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.6619 (mt0) REVERT: C 239 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7379 (mmmt) REVERT: E 93 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7652 (mttt) REVERT: E 102 MET cc_start: 0.4741 (OUTLIER) cc_final: 0.4265 (tpt) REVERT: E 140 MET cc_start: 0.7547 (tpt) cc_final: 0.7156 (tpt) REVERT: E 213 MET cc_start: 0.8008 (mtp) cc_final: 0.7720 (mtm) REVERT: E 216 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6968 (ptm160) REVERT: E 219 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: G 102 MET cc_start: 0.4616 (tpt) cc_final: 0.4326 (tpt) REVERT: G 173 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.5025 (mm-30) REVERT: G 216 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7239 (ptm160) REVERT: G 219 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.6546 (mt0) REVERT: H 213 MET cc_start: 0.8067 (mtp) cc_final: 0.7721 (mtm) REVERT: H 216 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.7156 (ptm-80) REVERT: I 93 LYS cc_start: 0.7541 (mttm) cc_final: 0.6751 (tttm) REVERT: I 102 MET cc_start: 0.4238 (tpt) cc_final: 0.3971 (tpt) REVERT: I 118 ASN cc_start: 0.6993 (t0) cc_final: 0.6765 (t0) REVERT: I 216 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.7240 (ptm160) REVERT: I 219 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6939 (mt0) REVERT: I 239 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7486 (mmmt) REVERT: J 137 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6954 (ppp) REVERT: J 216 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6994 (ptm160) REVERT: J 219 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6431 (mt0) REVERT: F 70 ASN cc_start: 0.6445 (OUTLIER) cc_final: 0.6154 (t0) REVERT: F 216 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6757 (ptm160) REVERT: F 219 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6691 (mt0) REVERT: F 239 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.6994 (mmmt) REVERT: D 173 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.4829 (mm-30) REVERT: D 216 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7290 (ptm160) REVERT: D 219 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6518 (mt0) REVERT: D 239 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7020 (mmpt) REVERT: K 1 MET cc_start: 0.5858 (OUTLIER) cc_final: 0.5534 (ptt) REVERT: N 12 MET cc_start: 0.6342 (ptt) cc_final: 0.5864 (ptt) REVERT: S 1 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.5436 (ptt) outliers start: 108 outliers final: 56 residues processed: 447 average time/residue: 1.4214 time to fit residues: 713.8645 Evaluate side-chains 481 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 393 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 216 ARG Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 239 LYS Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 35 SER Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 18 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER 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: 0.5980 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ** L 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN C 188 GLN E 188 GLN H 110 GLN H 188 GLN I 188 GLN J 188 GLN F 110 GLN F 188 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 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: 0.7054 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21850 Z= 0.200 Angle : 0.591 8.199 29570 Z= 0.305 Chirality : 0.048 0.206 3350 Planarity : 0.004 0.040 3710 Dihedral : 6.614 58.549 2980 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.83 % Allowed : 16.84 % Favored : 78.33 % 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: -0.63 (0.17), residues: 2610 helix: -0.23 (0.17), residues: 990 sheet: 0.37 (0.21), residues: 710 loop : -1.10 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 79 HIS 0.003 0.001 HIS F 144 PHE 0.018 0.002 PHE H 148 TYR 0.015 0.001 TYR C 75 ARG 0.008 0.001 ARG S 66 *********************** 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 516 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 403 time to evaluate : 2.562 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7505 (mttm) cc_final: 0.6657 (tttm) REVERT: A 102 MET cc_start: 0.4284 (tpt) cc_final: 0.4055 (tpt) REVERT: A 216 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7515 (ptm160) REVERT: A 221 MET cc_start: 0.6139 (ptp) cc_final: 0.5922 (ptp) REVERT: L 36 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7341 (tmtp) REVERT: B 93 LYS cc_start: 0.7529 (mttm) cc_final: 0.6627 (tttm) REVERT: B 137 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6859 (ppp) REVERT: B 216 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6913 (ptm160) REVERT: B 219 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.6485 (mt0) REVERT: C 102 MET cc_start: 0.4527 (tpt) cc_final: 0.4284 (tpt) REVERT: C 216 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.6874 (ptm160) REVERT: C 219 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6543 (mt0) REVERT: C 239 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7350 (mmmt) REVERT: C 246 THR cc_start: 0.8479 (m) cc_final: 0.8260 (p) REVERT: E 93 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7643 (mttt) REVERT: E 102 MET cc_start: 0.4731 (OUTLIER) cc_final: 0.4251 (tpt) REVERT: E 140 MET cc_start: 0.7578 (tpt) cc_final: 0.7051 (tpt) REVERT: E 213 MET cc_start: 0.8019 (mtp) cc_final: 0.7762 (mtm) REVERT: E 216 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7155 (ptm160) REVERT: E 219 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6845 (mt0) REVERT: G 173 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.4968 (mm-30) REVERT: G 216 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7217 (ptm160) REVERT: G 219 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6455 (mt0) REVERT: H 140 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.7012 (mmp) REVERT: H 213 MET cc_start: 0.8020 (mtp) cc_final: 0.7733 (mtm) REVERT: H 216 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7186 (ptm-80) REVERT: I 93 LYS cc_start: 0.7561 (mttm) cc_final: 0.6739 (tttm) REVERT: I 118 ASN cc_start: 0.6961 (t0) cc_final: 0.6752 (t0) REVERT: I 211 MET cc_start: 0.7291 (mmt) cc_final: 0.6637 (mtt) REVERT: I 216 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7113 (ptm160) REVERT: I 219 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6945 (mt0) REVERT: J 137 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6946 (ppp) REVERT: J 216 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6947 (ptm160) REVERT: J 219 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6421 (mt0) REVERT: F 70 ASN cc_start: 0.6458 (OUTLIER) cc_final: 0.6217 (t0) REVERT: F 216 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6757 (ptm160) REVERT: F 219 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6698 (mt0) REVERT: F 239 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7003 (mmmt) REVERT: D 173 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.4872 (mm-30) REVERT: D 216 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7354 (ptm160) REVERT: D 219 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6623 (mt0) REVERT: K 1 MET cc_start: 0.5925 (OUTLIER) cc_final: 0.5604 (ptt) REVERT: N 12 MET cc_start: 0.6340 (ptt) cc_final: 0.5852 (ptt) REVERT: N 38 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7314 (ttt180) REVERT: S 1 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5464 (ptt) outliers start: 113 outliers final: 61 residues processed: 449 average time/residue: 1.4234 time to fit residues: 717.7473 Evaluate side-chains 486 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 394 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 219 GLN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 216 ARG Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER 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: 8.9990 chunk 219 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 110 GLN H 188 GLN I 188 GLN J 188 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** ** 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: 0.7071 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21850 Z= 0.243 Angle : 0.617 7.922 29570 Z= 0.317 Chirality : 0.049 0.206 3350 Planarity : 0.004 0.039 3710 Dihedral : 6.655 59.482 2980 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.09 % Allowed : 16.75 % Favored : 78.16 % 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: -0.62 (0.17), residues: 2610 helix: -0.23 (0.17), residues: 990 sheet: 0.39 (0.21), residues: 710 loop : -1.09 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 79 HIS 0.004 0.001 HIS F 144 PHE 0.018 0.002 PHE H 148 TYR 0.015 0.002 TYR E 175 ARG 0.008 0.001 ARG S 66 *********************** 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 516 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 397 time to evaluate : 2.332 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7517 (mttm) cc_final: 0.6689 (tttm) REVERT: A 102 MET cc_start: 0.4171 (tpt) cc_final: 0.3915 (tpt) REVERT: A 216 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7476 (ptm160) REVERT: A 221 MET cc_start: 0.6285 (ptp) cc_final: 0.5983 (ptp) REVERT: L 36 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7369 (tmtp) REVERT: B 93 LYS cc_start: 0.7561 (mttm) cc_final: 0.6635 (tttm) REVERT: B 137 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6955 (ppp) REVERT: B 216 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6930 (ptm160) REVERT: B 219 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6530 (mt0) REVERT: C 102 MET cc_start: 0.4502 (tpt) cc_final: 0.4238 (tpt) REVERT: C 216 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.6885 (ptm160) REVERT: C 219 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6687 (mt0) REVERT: C 239 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7321 (mmmt) REVERT: C 246 THR cc_start: 0.8484 (m) cc_final: 0.8275 (p) REVERT: E 93 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7658 (mttt) REVERT: E 102 MET cc_start: 0.4762 (OUTLIER) cc_final: 0.4299 (tpt) REVERT: E 140 MET cc_start: 0.7626 (tpt) cc_final: 0.7129 (tpt) REVERT: E 213 MET cc_start: 0.8026 (mtp) cc_final: 0.7787 (mtm) REVERT: E 216 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7140 (ptm160) REVERT: E 239 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.6870 (mmmt) REVERT: G 173 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.4965 (mm-30) REVERT: G 216 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7206 (ptm160) REVERT: G 219 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6498 (mt0) REVERT: G 239 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7296 (mmpt) REVERT: H 213 MET cc_start: 0.8062 (mtp) cc_final: 0.7792 (mtm) REVERT: H 216 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7224 (ptm-80) REVERT: I 93 LYS cc_start: 0.7551 (mttm) cc_final: 0.6767 (tttm) REVERT: I 118 ASN cc_start: 0.6970 (t0) cc_final: 0.6751 (t0) REVERT: I 216 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7253 (ptm160) REVERT: I 219 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6933 (mt0) REVERT: J 137 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6956 (ppp) REVERT: J 216 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6968 (ptm160) REVERT: J 219 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.6439 (mt0) REVERT: F 70 ASN cc_start: 0.6522 (OUTLIER) cc_final: 0.6225 (t0) REVERT: F 216 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6814 (ptm160) REVERT: F 219 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6704 (mt0) REVERT: F 239 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.6985 (mmmt) REVERT: D 102 MET cc_start: 0.5004 (OUTLIER) cc_final: 0.4717 (ttt) REVERT: D 173 GLU cc_start: 0.5570 (OUTLIER) cc_final: 0.4867 (mm-30) REVERT: D 216 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7304 (ptm160) REVERT: D 219 GLN cc_start: 0.7103 (OUTLIER) cc_final: 0.6506 (mt0) REVERT: D 239 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.6963 (mmpt) REVERT: K 1 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5570 (ptt) REVERT: N 12 MET cc_start: 0.6325 (ptt) cc_final: 0.5851 (ptt) REVERT: S 1 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5477 (ptt) outliers start: 119 outliers final: 63 residues processed: 448 average time/residue: 1.4409 time to fit residues: 726.4913 Evaluate side-chains 486 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 390 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 75 TYR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 216 ARG Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.9980 chunk 246 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 259 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 110 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** T 75 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 21850 Z= 0.238 Angle : 0.618 8.271 29570 Z= 0.318 Chirality : 0.049 0.204 3350 Planarity : 0.004 0.038 3710 Dihedral : 6.636 58.552 2980 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.83 % Allowed : 17.14 % Favored : 78.03 % 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: -0.60 (0.17), residues: 2610 helix: -0.27 (0.17), residues: 990 sheet: 0.44 (0.21), residues: 710 loop : -1.04 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 79 HIS 0.003 0.001 HIS F 144 PHE 0.018 0.002 PHE H 148 TYR 0.019 0.002 TYR C 75 ARG 0.007 0.001 ARG S 66 ********************** 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 502 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 389 time to evaluate : 2.700 Fit side-chains revert: symmetry clash REVERT: A 93 LYS cc_start: 0.7520 (mttm) cc_final: 0.6694 (tttm) REVERT: A 102 MET cc_start: 0.4051 (tpt) cc_final: 0.3779 (tpt) REVERT: A 216 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7512 (ptm160) REVERT: A 221 MET cc_start: 0.6275 (ptp) cc_final: 0.5964 (ptp) REVERT: L 1 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.5173 (ptt) REVERT: B 93 LYS cc_start: 0.7555 (mttm) cc_final: 0.6627 (tttm) REVERT: B 137 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6944 (ppp) REVERT: B 216 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6906 (ptm160) REVERT: B 219 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6494 (mt0) REVERT: C 102 MET cc_start: 0.4512 (tpt) cc_final: 0.4286 (tpt) REVERT: C 216 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6862 (ptm160) REVERT: C 219 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6675 (mt0) REVERT: C 239 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7374 (mmmt) REVERT: C 246 THR cc_start: 0.8487 (m) cc_final: 0.8273 (p) REVERT: E 93 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7646 (mttt) REVERT: E 102 MET cc_start: 0.4749 (OUTLIER) cc_final: 0.4286 (tpt) REVERT: E 140 MET cc_start: 0.7610 (tpt) cc_final: 0.7090 (tpt) REVERT: E 211 MET cc_start: 0.6901 (mtt) cc_final: 0.6650 (mtt) REVERT: E 213 MET cc_start: 0.8053 (mtp) cc_final: 0.7793 (mtm) REVERT: E 216 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7140 (ptm160) REVERT: G 102 MET cc_start: 0.4621 (tpt) cc_final: 0.4386 (tpt) REVERT: G 173 GLU cc_start: 0.5589 (OUTLIER) cc_final: 0.4963 (mm-30) REVERT: G 216 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7208 (ptm160) REVERT: G 219 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.6510 (mt0) REVERT: G 239 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7300 (mmpt) REVERT: H 213 MET cc_start: 0.8023 (mtp) cc_final: 0.7775 (mtm) REVERT: H 216 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.7212 (ptm-80) REVERT: I 93 LYS cc_start: 0.7562 (mttm) cc_final: 0.6739 (tttm) REVERT: I 118 ASN cc_start: 0.6963 (t0) cc_final: 0.6751 (t0) REVERT: I 216 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7109 (ptm160) REVERT: I 219 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6950 (mt0) REVERT: J 102 MET cc_start: 0.4411 (tpt) cc_final: 0.3724 (tpt) REVERT: J 137 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6908 (ppp) REVERT: J 216 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6925 (ptm160) REVERT: J 219 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.6434 (mt0) REVERT: F 70 ASN cc_start: 0.6507 (OUTLIER) cc_final: 0.6237 (t0) REVERT: F 216 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6849 (ptm160) REVERT: F 219 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6704 (mt0) REVERT: F 239 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.6973 (mmmt) REVERT: D 102 MET cc_start: 0.5046 (OUTLIER) cc_final: 0.4756 (ttt) REVERT: D 173 GLU cc_start: 0.5637 (OUTLIER) cc_final: 0.4937 (mm-30) REVERT: D 216 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7325 (ptm160) REVERT: D 219 GLN cc_start: 0.7078 (OUTLIER) cc_final: 0.6590 (mt0) REVERT: D 239 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6977 (mmpt) REVERT: K 1 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5539 (ptt) REVERT: N 12 MET cc_start: 0.6305 (ptt) cc_final: 0.5847 (ptt) REVERT: S 1 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5459 (ptt) outliers start: 113 outliers final: 62 residues processed: 441 average time/residue: 1.4095 time to fit residues: 699.1687 Evaluate side-chains 480 residues out of total 2340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 386 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 216 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 249 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 216 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 129 MET Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 219 GLN Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 239 LYS Chi-restraints excluded: chain C residue 249 ARG Chi-restraints excluded: chain E residue 93 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 216 ARG Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 216 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 219 GLN Chi-restraints excluded: chain G residue 228 SER Chi-restraints excluded: chain G residue 239 LYS Chi-restraints excluded: chain H residue 129 MET Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 216 ARG Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 216 ARG Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 219 GLN Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 209 THR Chi-restraints excluded: chain J residue 216 ARG Chi-restraints excluded: chain J residue 218 VAL Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain F residue 70 ASN Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 216 ARG Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 GLN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 239 LYS Chi-restraints excluded: chain F residue 249 ARG Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 216 ARG Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 239 LYS Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 24 SER Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 24 SER Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 24 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 24 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain R residue 24 SER Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 24 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 30 optimal weight: 0.0670 chunk 57 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 212 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- 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 H 110 GLN H 188 GLN I 188 GLN J 188 GLN F 188 GLN ** N 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.213425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.190407 restraints weight = 21845.976| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 1.67 r_work: 0.4088 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3948 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21850 Z= 0.164 Angle : 0.570 7.870 29570 Z= 0.295 Chirality : 0.046 0.230 3350 Planarity : 0.004 0.041 3710 Dihedral : 6.423 55.620 2980 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.19 % Allowed : 18.16 % Favored : 77.65 % 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: -0.36 (0.17), residues: 2610 helix: -0.08 (0.18), residues: 990 sheet: 0.54 (0.21), residues: 710 loop : -0.90 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 79 HIS 0.004 0.001 HIS I 210 PHE 0.018 0.001 PHE H 148 TYR 0.012 0.001 TYR E 175 ARG 0.010 0.000 ARG K 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10302.66 seconds wall clock time: 182 minutes 22.10 seconds (10942.10 seconds total)