Starting phenix.real_space_refine on Tue Feb 20 12:36:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1y_21019/02_2024/6v1y_21019_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 120 5.16 5 C 18520 2.51 5 N 4552 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "B ARG 58": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "D ARG 58": "NH1" <-> "NH2" Residue "D ARG 165": "NH1" <-> "NH2" Residue "D ARG 176": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "M ARG 58": "NH1" <-> "NH2" Residue "M ARG 165": "NH1" <-> "NH2" Residue "M ARG 176": "NH1" <-> "NH2" Residue "M ARG 184": "NH1" <-> "NH2" Residue "M ARG 222": "NH1" <-> "NH2" Residue "M ARG 246": "NH1" <-> "NH2" Residue "M ARG 272": "NH1" <-> "NH2" Residue "M ARG 305": "NH1" <-> "NH2" Residue "M ARG 307": "NH1" <-> "NH2" Residue "M ARG 310": "NH1" <-> "NH2" Residue "M ARG 314": "NH1" <-> "NH2" Residue "N ARG 58": "NH1" <-> "NH2" Residue "N ARG 165": "NH1" <-> "NH2" Residue "N ARG 176": "NH1" <-> "NH2" Residue "N ARG 184": "NH1" <-> "NH2" Residue "N ARG 222": "NH1" <-> "NH2" Residue "N ARG 246": "NH1" <-> "NH2" Residue "N ARG 272": "NH1" <-> "NH2" Residue "N ARG 305": "NH1" <-> "NH2" Residue "N ARG 307": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "O ARG 58": "NH1" <-> "NH2" Residue "O ARG 165": "NH1" <-> "NH2" Residue "O ARG 176": "NH1" <-> "NH2" Residue "O ARG 184": "NH1" <-> "NH2" Residue "O ARG 222": "NH1" <-> "NH2" Residue "O ARG 246": "NH1" <-> "NH2" Residue "O ARG 272": "NH1" <-> "NH2" Residue "O ARG 305": "NH1" <-> "NH2" Residue "O ARG 307": "NH1" <-> "NH2" Residue "O ARG 310": "NH1" <-> "NH2" Residue "O ARG 314": "NH1" <-> "NH2" Residue "P ARG 58": "NH1" <-> "NH2" Residue "P ARG 165": "NH1" <-> "NH2" Residue "P ARG 176": "NH1" <-> "NH2" Residue "P ARG 184": "NH1" <-> "NH2" Residue "P ARG 222": "NH1" <-> "NH2" Residue "P ARG 246": "NH1" <-> "NH2" Residue "P ARG 272": "NH1" <-> "NH2" Residue "P ARG 305": "NH1" <-> "NH2" Residue "P ARG 307": "NH1" <-> "NH2" Residue "P ARG 310": "NH1" <-> "NH2" Residue "P ARG 314": "NH1" <-> "NH2" 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: 27896 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 180 Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 180 Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 180 Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 180 Chain: "M" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 180 Chain: "N" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 180 Chain: "O" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 180 Chain: "P" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 180 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNJ': 1, 'QNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.21, per 1000 atoms: 0.47 Number of scatterers: 27896 At special positions: 0 Unit cell: (115.976, 115.976, 226.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 8 15.00 O 4696 8.00 N 4552 7.00 C 18520 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: 10.75 Conformation dependent library (CDL) restraints added in 4.9 seconds 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 0 sheets defined 58.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 57 through 82 removed outlier: 3.545A pdb=" N ALA A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.675A pdb=" N ILE A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 162 through 187 removed outlier: 3.768A pdb=" N LEU A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP A 173 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG A 177 " --> pdb=" O TRP A 173 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.542A pdb=" N ARG A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 258 removed outlier: 3.633A pdb=" N THR A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 302 removed outlier: 3.957A pdb=" N ILE A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.661A pdb=" N ASN A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 345 through 353 Processing helix chain 'A' and resid 359 through 372 removed outlier: 3.765A pdb=" N PHE A 369 " --> pdb=" O ASN A 365 " (cutoff:3.500A) Proline residue: A 370 - end of helix Processing helix chain 'A' and resid 384 through 392 removed outlier: 4.172A pdb=" N GLN A 388 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP A 392 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 485 through 497 Processing helix chain 'B' and resid 57 through 82 removed outlier: 3.544A pdb=" N ALA B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) Proline residue: B 78 - end of helix Processing helix chain 'B' and resid 92 through 110 removed outlier: 3.676A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 162 through 187 removed outlier: 3.768A pdb=" N LEU B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG B 177 " --> pdb=" O TRP B 173 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 221 removed outlier: 3.542A pdb=" N ARG B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.632A pdb=" N THR B 257 " --> pdb=" O TRP B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 302 removed outlier: 3.957A pdb=" N ILE B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.662A pdb=" N ASN B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 342 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 359 through 372 removed outlier: 3.764A pdb=" N PHE B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) Proline residue: B 370 - end of helix Processing helix chain 'B' and resid 384 through 392 removed outlier: 4.172A pdb=" N GLN B 388 " --> pdb=" O ASN B 384 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 391 " --> pdb=" O PHE B 387 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP B 392 " --> pdb=" O GLN B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'C' and resid 57 through 82 removed outlier: 3.545A pdb=" N ALA C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Proline residue: C 78 - end of helix Processing helix chain 'C' and resid 92 through 110 removed outlier: 3.675A pdb=" N ILE C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 149 through 155 Processing helix chain 'C' and resid 162 through 187 removed outlier: 3.768A pdb=" N LEU C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 170 " --> pdb=" O ILE C 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP C 173 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG C 177 " --> pdb=" O TRP C 173 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU C 186 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 221 removed outlier: 3.542A pdb=" N ARG C 197 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 258 removed outlier: 3.633A pdb=" N THR C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 302 removed outlier: 3.957A pdb=" N ILE C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.661A pdb=" N ASN C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 342 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 359 through 372 removed outlier: 3.765A pdb=" N PHE C 369 " --> pdb=" O ASN C 365 " (cutoff:3.500A) Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 384 through 392 removed outlier: 4.172A pdb=" N GLN C 388 " --> pdb=" O ASN C 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER C 391 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP C 392 " --> pdb=" O GLN C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 472 through 477 Processing helix chain 'C' and resid 485 through 497 Processing helix chain 'D' and resid 57 through 82 removed outlier: 3.545A pdb=" N ALA D 61 " --> pdb=" O PRO D 57 " (cutoff:3.500A) Proline residue: D 78 - end of helix Processing helix chain 'D' and resid 92 through 110 removed outlier: 3.675A pdb=" N ILE D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 136 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 149 through 155 Processing helix chain 'D' and resid 162 through 187 removed outlier: 3.768A pdb=" N LEU D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP D 173 " --> pdb=" O MET D 169 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG D 177 " --> pdb=" O TRP D 173 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 221 removed outlier: 3.542A pdb=" N ARG D 197 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.633A pdb=" N THR D 257 " --> pdb=" O TRP D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 302 removed outlier: 3.957A pdb=" N ILE D 278 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 323 removed outlier: 3.661A pdb=" N ASN D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 342 Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 359 through 372 removed outlier: 3.765A pdb=" N PHE D 369 " --> pdb=" O ASN D 365 " (cutoff:3.500A) Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 384 through 392 removed outlier: 4.172A pdb=" N GLN D 388 " --> pdb=" O ASN D 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER D 391 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASP D 392 " --> pdb=" O GLN D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 485 through 497 Processing helix chain 'M' and resid 57 through 82 removed outlier: 3.546A pdb=" N ALA M 61 " --> pdb=" O PRO M 57 " (cutoff:3.500A) Proline residue: M 78 - end of helix Processing helix chain 'M' and resid 92 through 110 removed outlier: 3.675A pdb=" N ILE M 107 " --> pdb=" O ALA M 103 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE M 110 " --> pdb=" O ILE M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 136 Processing helix chain 'M' and resid 138 through 145 Processing helix chain 'M' and resid 149 through 155 Processing helix chain 'M' and resid 162 through 187 removed outlier: 3.768A pdb=" N LEU M 167 " --> pdb=" O GLY M 163 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU M 170 " --> pdb=" O ILE M 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU M 172 " --> pdb=" O SER M 168 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP M 173 " --> pdb=" O MET M 169 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG M 174 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU M 175 " --> pdb=" O ARG M 171 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARG M 176 " --> pdb=" O LEU M 172 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG M 177 " --> pdb=" O TRP M 173 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL M 178 " --> pdb=" O ARG M 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER M 179 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU M 186 " --> pdb=" O PHE M 182 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS M 187 " --> pdb=" O ALA M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 221 removed outlier: 3.542A pdb=" N ARG M 197 " --> pdb=" O TYR M 193 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N CYS M 198 " --> pdb=" O PHE M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 258 removed outlier: 3.633A pdb=" N THR M 257 " --> pdb=" O TRP M 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 302 removed outlier: 3.957A pdb=" N ILE M 278 " --> pdb=" O MET M 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE M 279 " --> pdb=" O LEU M 275 " (cutoff:3.500A) Processing helix chain 'M' and resid 305 through 323 removed outlier: 3.661A pdb=" N ASN M 323 " --> pdb=" O PHE M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 342 Processing helix chain 'M' and resid 345 through 353 Processing helix chain 'M' and resid 359 through 372 removed outlier: 3.765A pdb=" N PHE M 369 " --> pdb=" O ASN M 365 " (cutoff:3.500A) Proline residue: M 370 - end of helix Processing helix chain 'M' and resid 384 through 392 removed outlier: 4.172A pdb=" N GLN M 388 " --> pdb=" O ASN M 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER M 391 " --> pdb=" O PHE M 387 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP M 392 " --> pdb=" O GLN M 388 " (cutoff:3.500A) Processing helix chain 'M' and resid 447 through 449 No H-bonds generated for 'chain 'M' and resid 447 through 449' Processing helix chain 'M' and resid 472 through 477 Processing helix chain 'M' and resid 485 through 497 Processing helix chain 'N' and resid 57 through 82 removed outlier: 3.544A pdb=" N ALA N 61 " --> pdb=" O PRO N 57 " (cutoff:3.500A) Proline residue: N 78 - end of helix Processing helix chain 'N' and resid 92 through 110 removed outlier: 3.676A pdb=" N ILE N 107 " --> pdb=" O ALA N 103 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE N 110 " --> pdb=" O ILE N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 136 Processing helix chain 'N' and resid 138 through 145 Processing helix chain 'N' and resid 149 through 155 Processing helix chain 'N' and resid 162 through 187 removed outlier: 3.768A pdb=" N LEU N 167 " --> pdb=" O GLY N 163 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU N 170 " --> pdb=" O ILE N 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG N 171 " --> pdb=" O LEU N 167 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU N 172 " --> pdb=" O SER N 168 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TRP N 173 " --> pdb=" O MET N 169 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LEU N 175 " --> pdb=" O ARG N 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG N 176 " --> pdb=" O LEU N 172 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG N 177 " --> pdb=" O TRP N 173 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N VAL N 178 " --> pdb=" O ARG N 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER N 179 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU N 186 " --> pdb=" O PHE N 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS N 187 " --> pdb=" O ALA N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 193 through 221 removed outlier: 3.542A pdb=" N ARG N 197 " --> pdb=" O TYR N 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS N 198 " --> pdb=" O PHE N 194 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 258 removed outlier: 3.632A pdb=" N THR N 257 " --> pdb=" O TRP N 253 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 302 removed outlier: 3.957A pdb=" N ILE N 278 " --> pdb=" O MET N 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE N 279 " --> pdb=" O LEU N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 305 through 323 removed outlier: 3.662A pdb=" N ASN N 323 " --> pdb=" O PHE N 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 342 Processing helix chain 'N' and resid 345 through 353 Processing helix chain 'N' and resid 359 through 372 removed outlier: 3.764A pdb=" N PHE N 369 " --> pdb=" O ASN N 365 " (cutoff:3.500A) Proline residue: N 370 - end of helix Processing helix chain 'N' and resid 384 through 392 removed outlier: 4.172A pdb=" N GLN N 388 " --> pdb=" O ASN N 384 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER N 391 " --> pdb=" O PHE N 387 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP N 392 " --> pdb=" O GLN N 388 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 449 No H-bonds generated for 'chain 'N' and resid 447 through 449' Processing helix chain 'N' and resid 472 through 477 Processing helix chain 'N' and resid 485 through 497 Processing helix chain 'O' and resid 57 through 82 removed outlier: 3.544A pdb=" N ALA O 61 " --> pdb=" O PRO O 57 " (cutoff:3.500A) Proline residue: O 78 - end of helix Processing helix chain 'O' and resid 92 through 110 removed outlier: 3.675A pdb=" N ILE O 107 " --> pdb=" O ALA O 103 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE O 110 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 136 Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 155 Processing helix chain 'O' and resid 162 through 187 removed outlier: 3.768A pdb=" N LEU O 167 " --> pdb=" O GLY O 163 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU O 170 " --> pdb=" O ILE O 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG O 171 " --> pdb=" O LEU O 167 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU O 172 " --> pdb=" O SER O 168 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP O 173 " --> pdb=" O MET O 169 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG O 174 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU O 175 " --> pdb=" O ARG O 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG O 176 " --> pdb=" O LEU O 172 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG O 177 " --> pdb=" O TRP O 173 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL O 178 " --> pdb=" O ARG O 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER O 179 " --> pdb=" O LEU O 175 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU O 186 " --> pdb=" O PHE O 182 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS O 187 " --> pdb=" O ALA O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 221 removed outlier: 3.542A pdb=" N ARG O 197 " --> pdb=" O TYR O 193 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N CYS O 198 " --> pdb=" O PHE O 194 " (cutoff:3.500A) Processing helix chain 'O' and resid 243 through 258 removed outlier: 3.633A pdb=" N THR O 257 " --> pdb=" O TRP O 253 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 302 removed outlier: 3.957A pdb=" N ILE O 278 " --> pdb=" O MET O 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE O 279 " --> pdb=" O LEU O 275 " (cutoff:3.500A) Processing helix chain 'O' and resid 305 through 323 removed outlier: 3.661A pdb=" N ASN O 323 " --> pdb=" O PHE O 319 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 342 Processing helix chain 'O' and resid 345 through 353 Processing helix chain 'O' and resid 359 through 372 removed outlier: 3.765A pdb=" N PHE O 369 " --> pdb=" O ASN O 365 " (cutoff:3.500A) Proline residue: O 370 - end of helix Processing helix chain 'O' and resid 384 through 392 removed outlier: 4.172A pdb=" N GLN O 388 " --> pdb=" O ASN O 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER O 391 " --> pdb=" O PHE O 387 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP O 392 " --> pdb=" O GLN O 388 " (cutoff:3.500A) Processing helix chain 'O' and resid 447 through 449 No H-bonds generated for 'chain 'O' and resid 447 through 449' Processing helix chain 'O' and resid 472 through 477 Processing helix chain 'O' and resid 485 through 497 Processing helix chain 'P' and resid 57 through 82 removed outlier: 3.545A pdb=" N ALA P 61 " --> pdb=" O PRO P 57 " (cutoff:3.500A) Proline residue: P 78 - end of helix Processing helix chain 'P' and resid 92 through 110 removed outlier: 3.675A pdb=" N ILE P 107 " --> pdb=" O ALA P 103 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE P 110 " --> pdb=" O ILE P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 136 Processing helix chain 'P' and resid 138 through 145 Processing helix chain 'P' and resid 149 through 155 Processing helix chain 'P' and resid 162 through 187 removed outlier: 3.768A pdb=" N LEU P 167 " --> pdb=" O GLY P 163 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU P 170 " --> pdb=" O ILE P 166 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ARG P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU P 172 " --> pdb=" O SER P 168 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N TRP P 173 " --> pdb=" O MET P 169 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ARG P 174 " --> pdb=" O LEU P 170 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU P 175 " --> pdb=" O ARG P 171 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG P 176 " --> pdb=" O LEU P 172 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG P 177 " --> pdb=" O TRP P 173 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL P 178 " --> pdb=" O ARG P 174 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER P 179 " --> pdb=" O LEU P 175 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU P 186 " --> pdb=" O PHE P 182 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS P 187 " --> pdb=" O ALA P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 221 removed outlier: 3.542A pdb=" N ARG P 197 " --> pdb=" O TYR P 193 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N CYS P 198 " --> pdb=" O PHE P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 258 removed outlier: 3.633A pdb=" N THR P 257 " --> pdb=" O TRP P 253 " (cutoff:3.500A) Processing helix chain 'P' and resid 271 through 302 removed outlier: 3.956A pdb=" N ILE P 278 " --> pdb=" O MET P 274 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) Processing helix chain 'P' and resid 305 through 323 removed outlier: 3.661A pdb=" N ASN P 323 " --> pdb=" O PHE P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 328 through 342 Processing helix chain 'P' and resid 345 through 353 Processing helix chain 'P' and resid 359 through 372 removed outlier: 3.766A pdb=" N PHE P 369 " --> pdb=" O ASN P 365 " (cutoff:3.500A) Proline residue: P 370 - end of helix Processing helix chain 'P' and resid 384 through 392 removed outlier: 4.172A pdb=" N GLN P 388 " --> pdb=" O ASN P 384 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASP P 392 " --> pdb=" O GLN P 388 " (cutoff:3.500A) Processing helix chain 'P' and resid 447 through 449 No H-bonds generated for 'chain 'P' and resid 447 through 449' Processing helix chain 'P' and resid 472 through 477 Processing helix chain 'P' and resid 485 through 497 1280 hydrogen bonds defined for protein. 3840 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: 7.61 Time building geometry restraints manager: 11.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4048 1.29 - 1.42: 8455 1.42 - 1.55: 15953 1.55 - 1.67: 64 1.67 - 1.80: 192 Bond restraints: 28712 Sorted by residual: bond pdb=" C PRO O 150 " pdb=" N LEU O 151 " ideal model delta sigma weight residual 1.334 1.497 -0.162 1.43e-02 4.89e+03 1.29e+02 bond pdb=" C PRO B 150 " pdb=" N LEU B 151 " ideal model delta sigma weight residual 1.334 1.496 -0.162 1.43e-02 4.89e+03 1.29e+02 bond pdb=" C PRO N 150 " pdb=" N LEU N 151 " ideal model delta sigma weight residual 1.334 1.496 -0.162 1.43e-02 4.89e+03 1.28e+02 bond pdb=" C PRO C 150 " pdb=" N LEU C 151 " ideal model delta sigma weight residual 1.334 1.497 -0.163 1.46e-02 4.69e+03 1.24e+02 bond pdb=" C PRO D 150 " pdb=" N LEU D 151 " ideal model delta sigma weight residual 1.334 1.497 -0.163 1.46e-02 4.69e+03 1.24e+02 ... (remaining 28707 not shown) Histogram of bond angle deviations from ideal: 95.22 - 102.99: 247 102.99 - 110.76: 9519 110.76 - 118.53: 12535 118.53 - 126.30: 16387 126.30 - 134.07: 576 Bond angle restraints: 39264 Sorted by residual: angle pdb=" C THR N 259 " pdb=" N THR N 260 " pdb=" CA THR N 260 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C THR O 259 " pdb=" N THR O 260 " pdb=" CA THR O 260 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C THR B 259 " pdb=" N THR B 260 " pdb=" CA THR B 260 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C THR P 259 " pdb=" N THR P 260 " pdb=" CA THR P 260 " ideal model delta sigma weight residual 121.54 130.10 -8.56 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C THR A 259 " pdb=" N THR A 260 " pdb=" CA THR A 260 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 ... (remaining 39259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 15599 15.08 - 30.17: 1097 30.17 - 45.25: 224 45.25 - 60.34: 64 60.34 - 75.42: 8 Dihedral angle restraints: 16992 sinusoidal: 6408 harmonic: 10584 Sorted by residual: dihedral pdb=" CA SER B 125 " pdb=" C SER B 125 " pdb=" N PRO B 126 " pdb=" CA PRO B 126 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER N 125 " pdb=" C SER N 125 " pdb=" N PRO N 126 " pdb=" CA PRO N 126 " ideal model delta harmonic sigma weight residual 180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA SER D 125 " pdb=" C SER D 125 " pdb=" N PRO D 126 " pdb=" CA PRO D 126 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 16989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3767 0.084 - 0.168: 634 0.168 - 0.253: 71 0.253 - 0.337: 32 0.337 - 0.421: 8 Chirality restraints: 4512 Sorted by residual: chirality pdb=" C10 QNJ O 601 " pdb=" C1 QNJ O 601 " pdb=" C5 QNJ O 601 " pdb=" C9 QNJ O 601 " both_signs ideal model delta sigma weight residual False -2.91 -2.49 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C10 QNJ N 602 " pdb=" C1 QNJ N 602 " pdb=" C5 QNJ N 602 " pdb=" C9 QNJ N 602 " both_signs ideal model delta sigma weight residual False -2.91 -2.49 -0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C10 QNJ D 601 " pdb=" C1 QNJ D 601 " pdb=" C5 QNJ D 601 " pdb=" C9 QNJ D 601 " both_signs ideal model delta sigma weight residual False -2.91 -2.49 -0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 4509 not shown) Planarity restraints: 4824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL O 439 " -0.015 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C VAL O 439 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL O 439 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE O 440 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 439 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C VAL B 439 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL B 439 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE B 440 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 439 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C VAL P 439 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL P 439 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE P 440 " -0.018 2.00e-02 2.50e+03 ... (remaining 4821 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7705 2.80 - 3.33: 25926 3.33 - 3.85: 43532 3.85 - 4.38: 46960 4.38 - 4.90: 82309 Nonbonded interactions: 206432 Sorted by model distance: nonbonded pdb=" O ALA N 358 " pdb=" OG SER N 361 " model vdw 2.278 2.440 nonbonded pdb=" O ALA B 358 " pdb=" OG SER B 361 " model vdw 2.279 2.440 nonbonded pdb=" O ALA O 358 " pdb=" OG SER O 361 " model vdw 2.280 2.440 nonbonded pdb=" O ALA C 358 " pdb=" OG SER C 361 " model vdw 2.280 2.440 nonbonded pdb=" O ALA D 358 " pdb=" OG SER D 361 " model vdw 2.280 2.440 ... (remaining 206427 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 50 through 498) selection = (chain 'B' and resid 50 through 498) selection = (chain 'C' and resid 50 through 498) selection = (chain 'D' and resid 50 through 498) selection = (chain 'M' and resid 50 through 498) selection = (chain 'N' and resid 50 through 498) selection = (chain 'O' and resid 50 through 498) selection = (chain 'P' and resid 50 through 498) } 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 group one per residue 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.390 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 67.410 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.200 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 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 : 0.011 0.163 28712 Z= 0.692 Angle : 1.194 10.098 39264 Z= 0.654 Chirality : 0.069 0.421 4512 Planarity : 0.008 0.060 4824 Dihedral : 11.549 75.420 10128 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.50 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % 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: -3.80 (0.12), residues: 3536 helix: -2.08 (0.09), residues: 2000 sheet: -2.22 (0.36), residues: 192 loop : -3.08 (0.15), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP O 75 HIS 0.014 0.003 HIS P 301 PHE 0.025 0.003 PHE M 92 TYR 0.035 0.003 TYR A 223 ARG 0.005 0.001 ARG M 322 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 743 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 TRP cc_start: 0.8428 (t-100) cc_final: 0.8071 (t60) REVERT: A 301 HIS cc_start: 0.7388 (t70) cc_final: 0.7178 (t-90) REVERT: B 58 ARG cc_start: 0.5432 (tpt170) cc_final: 0.5195 (tmt170) REVERT: B 173 TRP cc_start: 0.8454 (t-100) cc_final: 0.8020 (t60) REVERT: C 173 TRP cc_start: 0.8425 (t-100) cc_final: 0.8065 (t60) REVERT: C 301 HIS cc_start: 0.7418 (t70) cc_final: 0.7175 (t-90) REVERT: D 173 TRP cc_start: 0.8431 (t-100) cc_final: 0.8067 (t60) REVERT: D 301 HIS cc_start: 0.7410 (t70) cc_final: 0.7168 (t-90) REVERT: M 58 ARG cc_start: 0.6097 (tpt170) cc_final: 0.5476 (tmt170) REVERT: M 95 ASP cc_start: 0.8222 (m-30) cc_final: 0.7870 (t0) REVERT: M 302 TRP cc_start: 0.7894 (t-100) cc_final: 0.7679 (t60) REVERT: N 58 ARG cc_start: 0.6077 (tpt170) cc_final: 0.5467 (tmt170) REVERT: N 96 ASN cc_start: 0.8428 (m-40) cc_final: 0.8110 (m110) REVERT: N 302 TRP cc_start: 0.7943 (t-100) cc_final: 0.7718 (t60) REVERT: N 476 MET cc_start: 0.7270 (mmm) cc_final: 0.7028 (mmm) REVERT: O 58 ARG cc_start: 0.6082 (tpt170) cc_final: 0.5430 (tmt170) REVERT: O 95 ASP cc_start: 0.8227 (m-30) cc_final: 0.7946 (t0) REVERT: O 133 TYR cc_start: 0.8290 (t80) cc_final: 0.8083 (t80) REVERT: O 302 TRP cc_start: 0.7912 (t-100) cc_final: 0.7705 (t60) REVERT: P 58 ARG cc_start: 0.6072 (tpt170) cc_final: 0.5459 (tmt170) REVERT: P 95 ASP cc_start: 0.8230 (m-30) cc_final: 0.7879 (t0) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 0.4076 time to fit residues: 464.8031 Evaluate side-chains 440 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 106 optimal weight: 0.4980 chunk 167 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 319 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 99 ASN A 354 ASN B 56 ASN B 99 ASN B 332 GLN B 354 ASN C 56 ASN C 99 ASN C 354 ASN D 56 ASN D 99 ASN D 354 ASN M 56 ASN M 332 GLN M 354 ASN N 56 ASN N 332 GLN N 354 ASN N 491 ASN O 56 ASN O 332 GLN O 354 ASN O 491 ASN P 56 ASN P 332 GLN P 354 ASN P 491 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28712 Z= 0.230 Angle : 0.639 6.723 39264 Z= 0.338 Chirality : 0.043 0.153 4512 Planarity : 0.005 0.041 4824 Dihedral : 8.868 84.087 4720 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.78 % Favored : 91.97 % Rotamer: Outliers : 4.38 % Allowed : 10.05 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.14), residues: 3536 helix: 0.02 (0.11), residues: 2040 sheet: -2.49 (0.34), residues: 192 loop : -2.71 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 253 HIS 0.004 0.001 HIS N 301 PHE 0.018 0.002 PHE N 92 TYR 0.032 0.002 TYR P 376 ARG 0.007 0.001 ARG O 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 487 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.7330 (mmm) cc_final: 0.6918 (mmt) REVERT: A 92 PHE cc_start: 0.8391 (t80) cc_final: 0.8143 (t80) REVERT: A 105 ASP cc_start: 0.7800 (t0) cc_final: 0.7456 (t70) REVERT: A 143 CYS cc_start: 0.8170 (m) cc_final: 0.7864 (m) REVERT: A 295 MET cc_start: 0.8236 (mmt) cc_final: 0.8026 (mmt) REVERT: A 301 HIS cc_start: 0.7622 (t70) cc_final: 0.7315 (t-90) REVERT: B 58 ARG cc_start: 0.5459 (tpt170) cc_final: 0.5202 (tmt170) REVERT: B 64 MET cc_start: 0.7355 (mmm) cc_final: 0.6993 (mmt) REVERT: B 92 PHE cc_start: 0.8324 (t80) cc_final: 0.8082 (t80) REVERT: B 105 ASP cc_start: 0.7874 (t0) cc_final: 0.7578 (t70) REVERT: B 295 MET cc_start: 0.8257 (mmt) cc_final: 0.8053 (mmt) REVERT: B 415 TYR cc_start: 0.6254 (m-10) cc_final: 0.5971 (m-10) REVERT: C 64 MET cc_start: 0.7346 (mmm) cc_final: 0.6932 (mmt) REVERT: C 92 PHE cc_start: 0.8393 (t80) cc_final: 0.8148 (t80) REVERT: C 105 ASP cc_start: 0.7774 (t0) cc_final: 0.7430 (t70) REVERT: C 143 CYS cc_start: 0.8171 (m) cc_final: 0.7861 (m) REVERT: C 295 MET cc_start: 0.8252 (mmt) cc_final: 0.8039 (mmt) REVERT: C 301 HIS cc_start: 0.7616 (t70) cc_final: 0.7325 (t-90) REVERT: D 64 MET cc_start: 0.7348 (mmm) cc_final: 0.6920 (mmt) REVERT: D 92 PHE cc_start: 0.8404 (t80) cc_final: 0.8154 (t80) REVERT: D 105 ASP cc_start: 0.7786 (t0) cc_final: 0.7439 (t70) REVERT: D 143 CYS cc_start: 0.8165 (m) cc_final: 0.7862 (m) REVERT: D 295 MET cc_start: 0.8240 (mmt) cc_final: 0.8032 (mmt) REVERT: D 301 HIS cc_start: 0.7616 (t70) cc_final: 0.7321 (t-90) REVERT: M 58 ARG cc_start: 0.6485 (tpt170) cc_final: 0.5603 (ttt-90) REVERT: M 95 ASP cc_start: 0.8277 (m-30) cc_final: 0.7912 (t0) REVERT: M 96 ASN cc_start: 0.8313 (m-40) cc_final: 0.8104 (m110) REVERT: M 149 GLN cc_start: 0.8055 (pt0) cc_final: 0.7519 (mm-40) REVERT: M 173 TRP cc_start: 0.8649 (t-100) cc_final: 0.8426 (t-100) REVERT: M 270 ASN cc_start: 0.8163 (t0) cc_final: 0.7871 (m-40) REVERT: M 302 TRP cc_start: 0.8074 (t-100) cc_final: 0.7662 (t60) REVERT: N 58 ARG cc_start: 0.6458 (tpt170) cc_final: 0.5628 (ttt-90) REVERT: N 96 ASN cc_start: 0.8260 (m-40) cc_final: 0.8037 (m110) REVERT: N 270 ASN cc_start: 0.8163 (t0) cc_final: 0.7914 (m-40) REVERT: N 302 TRP cc_start: 0.8050 (t-100) cc_final: 0.7677 (t60) REVERT: O 58 ARG cc_start: 0.6380 (tpt170) cc_final: 0.5530 (ttt-90) REVERT: O 95 ASP cc_start: 0.8365 (m-30) cc_final: 0.7975 (t0) REVERT: O 149 GLN cc_start: 0.7301 (mm110) cc_final: 0.7050 (mm-40) REVERT: O 173 TRP cc_start: 0.8629 (t-100) cc_final: 0.8426 (t-100) REVERT: O 270 ASN cc_start: 0.8239 (t0) cc_final: 0.7881 (m-40) REVERT: O 302 TRP cc_start: 0.8080 (t-100) cc_final: 0.7681 (t60) REVERT: P 58 ARG cc_start: 0.6473 (tpt170) cc_final: 0.5589 (ttt-90) REVERT: P 96 ASN cc_start: 0.8297 (m-40) cc_final: 0.8066 (m110) REVERT: P 149 GLN cc_start: 0.8080 (pt0) cc_final: 0.7572 (mm-40) REVERT: P 173 TRP cc_start: 0.8651 (t-100) cc_final: 0.8425 (t-100) REVERT: P 270 ASN cc_start: 0.8214 (t0) cc_final: 0.7932 (m-40) outliers start: 116 outliers final: 56 residues processed: 572 average time/residue: 0.3519 time to fit residues: 327.3671 Evaluate side-chains 466 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 410 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain M residue 259 THR Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 259 THR Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 109 THR Chi-restraints excluded: chain O residue 259 THR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 109 THR Chi-restraints excluded: chain P residue 259 THR Chi-restraints excluded: chain P residue 381 VAL Chi-restraints excluded: chain P residue 473 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 266 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 345 optimal weight: 20.0000 chunk 285 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 491 ASN ** N 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 301 HIS ** O 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 28712 Z= 0.313 Angle : 0.674 10.294 39264 Z= 0.352 Chirality : 0.044 0.152 4512 Planarity : 0.004 0.048 4824 Dihedral : 8.650 85.682 4720 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.34 % Favored : 91.32 % Rotamer: Outliers : 4.15 % Allowed : 13.29 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.14), residues: 3536 helix: 0.65 (0.11), residues: 2032 sheet: -2.60 (0.34), residues: 192 loop : -2.57 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP O 253 HIS 0.006 0.001 HIS B 336 PHE 0.015 0.002 PHE P 92 TYR 0.028 0.002 TYR P 376 ARG 0.004 0.001 ARG O 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 456 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 HIS cc_start: 0.7828 (t70) cc_final: 0.7444 (t-90) REVERT: B 58 ARG cc_start: 0.5596 (tpt170) cc_final: 0.5238 (tmt170) REVERT: B 105 ASP cc_start: 0.7838 (t0) cc_final: 0.7401 (t70) REVERT: B 397 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: B 415 TYR cc_start: 0.6453 (m-10) cc_final: 0.5988 (m-10) REVERT: C 301 HIS cc_start: 0.7848 (t70) cc_final: 0.7457 (t-90) REVERT: D 301 HIS cc_start: 0.7841 (t70) cc_final: 0.7452 (t-90) REVERT: M 58 ARG cc_start: 0.6788 (tpt170) cc_final: 0.5669 (tmt170) REVERT: M 149 GLN cc_start: 0.8106 (pt0) cc_final: 0.7635 (mm-40) REVERT: N 58 ARG cc_start: 0.6783 (tpt170) cc_final: 0.5666 (tmt170) REVERT: O 58 ARG cc_start: 0.6670 (tpt170) cc_final: 0.5480 (tmt170) REVERT: P 58 ARG cc_start: 0.6749 (tpt170) cc_final: 0.5627 (tmt170) REVERT: P 149 GLN cc_start: 0.8125 (pt0) cc_final: 0.7624 (mm-40) outliers start: 110 outliers final: 80 residues processed: 547 average time/residue: 0.3927 time to fit residues: 350.2485 Evaluate side-chains 477 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 396 time to evaluate : 3.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 299 VAL Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 257 THR Chi-restraints excluded: chain N residue 296 THR Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 464 LEU Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 257 THR Chi-restraints excluded: chain O residue 296 THR Chi-restraints excluded: chain O residue 299 VAL Chi-restraints excluded: chain O residue 339 LEU Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain O residue 464 LEU Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 299 VAL Chi-restraints excluded: chain P residue 339 LEU Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 473 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 7.9990 chunk 240 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 152 optimal weight: 1.9990 chunk 215 optimal weight: 0.0060 chunk 321 optimal weight: 1.9990 chunk 340 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 28712 Z= 0.166 Angle : 0.554 6.531 39264 Z= 0.289 Chirality : 0.042 0.179 4512 Planarity : 0.003 0.044 4824 Dihedral : 7.929 87.172 4720 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.76 % Favored : 92.90 % Rotamer: Outliers : 3.25 % Allowed : 15.97 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.15), residues: 3536 helix: 1.03 (0.12), residues: 2072 sheet: -2.57 (0.34), residues: 192 loop : -2.39 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 75 HIS 0.002 0.001 HIS B 336 PHE 0.010 0.001 PHE O 138 TYR 0.023 0.001 TYR P 376 ARG 0.005 0.000 ARG O 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 480 time to evaluate : 3.235 Fit side-chains REVERT: A 64 MET cc_start: 0.6939 (mmt) cc_final: 0.6661 (mmt) REVERT: A 301 HIS cc_start: 0.7629 (t70) cc_final: 0.7365 (t-90) REVERT: B 58 ARG cc_start: 0.5388 (tpt170) cc_final: 0.5075 (tmt170) REVERT: B 64 MET cc_start: 0.6927 (mmt) cc_final: 0.6633 (mmt) REVERT: B 397 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: B 415 TYR cc_start: 0.6367 (m-10) cc_final: 0.5852 (m-10) REVERT: B 476 MET cc_start: 0.7496 (mmm) cc_final: 0.7216 (mmm) REVERT: C 64 MET cc_start: 0.6963 (mmt) cc_final: 0.6686 (mmt) REVERT: C 301 HIS cc_start: 0.7650 (t70) cc_final: 0.7376 (t-90) REVERT: D 64 MET cc_start: 0.6962 (mmt) cc_final: 0.6682 (mmt) REVERT: D 301 HIS cc_start: 0.7633 (t70) cc_final: 0.7371 (t-90) REVERT: M 58 ARG cc_start: 0.6699 (tpt170) cc_final: 0.5522 (tmt170) REVERT: M 75 TRP cc_start: 0.7947 (t60) cc_final: 0.7396 (t60) REVERT: M 149 GLN cc_start: 0.8123 (pt0) cc_final: 0.7617 (mm-40) REVERT: M 258 LEU cc_start: 0.9359 (tp) cc_final: 0.9104 (tt) REVERT: M 284 ASN cc_start: 0.8280 (t0) cc_final: 0.7928 (t0) REVERT: M 324 GLN cc_start: 0.8588 (mt0) cc_final: 0.8385 (mt0) REVERT: N 58 ARG cc_start: 0.6693 (tpt170) cc_final: 0.5517 (tmt170) REVERT: N 149 GLN cc_start: 0.7942 (pt0) cc_final: 0.7219 (mm-40) REVERT: N 258 LEU cc_start: 0.9344 (tp) cc_final: 0.9113 (tt) REVERT: N 284 ASN cc_start: 0.8239 (t0) cc_final: 0.7740 (t0) REVERT: N 397 TYR cc_start: 0.7304 (OUTLIER) cc_final: 0.6794 (t80) REVERT: O 58 ARG cc_start: 0.6672 (tpt170) cc_final: 0.5489 (tmt170) REVERT: O 75 TRP cc_start: 0.7957 (t60) cc_final: 0.7395 (t60) REVERT: O 106 ILE cc_start: 0.8719 (tp) cc_final: 0.8082 (tt) REVERT: O 258 LEU cc_start: 0.9330 (tp) cc_final: 0.9094 (tt) REVERT: O 284 ASN cc_start: 0.8251 (t0) cc_final: 0.7708 (t0) REVERT: O 324 GLN cc_start: 0.8585 (mt0) cc_final: 0.8380 (mt0) REVERT: P 58 ARG cc_start: 0.6704 (tpt170) cc_final: 0.5536 (tmt170) REVERT: P 149 GLN cc_start: 0.8128 (pt0) cc_final: 0.7611 (mm-40) REVERT: P 258 LEU cc_start: 0.9348 (tp) cc_final: 0.9112 (tt) REVERT: P 284 ASN cc_start: 0.8232 (t0) cc_final: 0.7707 (t0) REVERT: P 324 GLN cc_start: 0.8591 (mt0) cc_final: 0.8373 (mt0) outliers start: 86 outliers final: 59 residues processed: 535 average time/residue: 0.3531 time to fit residues: 306.0651 Evaluate side-chains 483 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 422 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 141 ASP Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 ASP Chi-restraints excluded: chain N residue 296 THR Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 221 ASP Chi-restraints excluded: chain O residue 296 THR Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 221 ASP Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 290 optimal weight: 2.9990 chunk 235 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 305 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN A 332 GLN A 349 GLN B 330 GLN C 332 GLN C 349 GLN D 330 GLN D 332 GLN D 349 GLN O 96 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28712 Z= 0.188 Angle : 0.560 8.085 39264 Z= 0.292 Chirality : 0.042 0.193 4512 Planarity : 0.003 0.033 4824 Dihedral : 7.538 80.919 4720 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.04 % Favored : 92.68 % Rotamer: Outliers : 3.74 % Allowed : 15.71 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.34 (0.15), residues: 3536 helix: 1.16 (0.12), residues: 2072 sheet: -1.86 (0.49), residues: 80 loop : -2.38 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 75 HIS 0.003 0.001 HIS B 336 PHE 0.011 0.001 PHE O 138 TYR 0.026 0.001 TYR B 376 ARG 0.006 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 452 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.7061 (mmt) cc_final: 0.6842 (mmt) REVERT: A 301 HIS cc_start: 0.7675 (t70) cc_final: 0.7399 (t-90) REVERT: B 58 ARG cc_start: 0.5457 (tpt170) cc_final: 0.5107 (tmt170) REVERT: B 64 MET cc_start: 0.6956 (mmt) cc_final: 0.6741 (mmt) REVERT: B 295 MET cc_start: 0.8165 (mmt) cc_final: 0.7841 (mmt) REVERT: B 397 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: B 415 TYR cc_start: 0.6320 (m-10) cc_final: 0.5818 (m-10) REVERT: B 476 MET cc_start: 0.7472 (mmm) cc_final: 0.7195 (mmm) REVERT: C 64 MET cc_start: 0.7087 (mmt) cc_final: 0.6853 (mmt) REVERT: C 277 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8720 (m-30) REVERT: C 301 HIS cc_start: 0.7696 (t70) cc_final: 0.7422 (t-90) REVERT: D 64 MET cc_start: 0.7086 (mmt) cc_final: 0.6857 (mmt) REVERT: D 277 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8731 (m-30) REVERT: D 301 HIS cc_start: 0.7679 (t70) cc_final: 0.7413 (t-90) REVERT: M 58 ARG cc_start: 0.6740 (tpt170) cc_final: 0.5598 (tmt170) REVERT: M 149 GLN cc_start: 0.8104 (pt0) cc_final: 0.7505 (mm-40) REVERT: M 257 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.9044 (m) REVERT: M 258 LEU cc_start: 0.9381 (tp) cc_final: 0.9047 (tt) REVERT: M 284 ASN cc_start: 0.8262 (t0) cc_final: 0.7909 (t0) REVERT: N 58 ARG cc_start: 0.6737 (tpt170) cc_final: 0.5592 (tmt170) REVERT: N 149 GLN cc_start: 0.7976 (pt0) cc_final: 0.7214 (mm-40) REVERT: N 258 LEU cc_start: 0.9365 (tp) cc_final: 0.9115 (tt) REVERT: N 273 GLU cc_start: 0.7562 (tt0) cc_final: 0.7276 (tt0) REVERT: N 284 ASN cc_start: 0.8269 (t0) cc_final: 0.7907 (t0) REVERT: N 397 TYR cc_start: 0.7342 (OUTLIER) cc_final: 0.6828 (t80) REVERT: O 257 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9101 (m) REVERT: O 258 LEU cc_start: 0.9351 (tp) cc_final: 0.9039 (tt) REVERT: O 284 ASN cc_start: 0.8212 (t0) cc_final: 0.7727 (t0) REVERT: P 58 ARG cc_start: 0.6723 (tpt170) cc_final: 0.5586 (tmt170) REVERT: P 149 GLN cc_start: 0.8138 (pt0) cc_final: 0.7505 (mm-40) REVERT: P 257 THR cc_start: 0.9342 (OUTLIER) cc_final: 0.9082 (m) REVERT: P 258 LEU cc_start: 0.9364 (tp) cc_final: 0.9066 (tt) REVERT: P 284 ASN cc_start: 0.8236 (t0) cc_final: 0.7883 (t0) outliers start: 99 outliers final: 70 residues processed: 516 average time/residue: 0.3433 time to fit residues: 290.5857 Evaluate side-chains 505 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 428 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 331 ASP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain M residue 80 GLN Chi-restraints excluded: chain M residue 141 ASP Chi-restraints excluded: chain M residue 151 LEU Chi-restraints excluded: chain M residue 221 ASP Chi-restraints excluded: chain M residue 257 THR Chi-restraints excluded: chain M residue 296 THR Chi-restraints excluded: chain M residue 327 HIS Chi-restraints excluded: chain M residue 335 SER Chi-restraints excluded: chain M residue 339 LEU Chi-restraints excluded: chain M residue 381 VAL Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain N residue 151 LEU Chi-restraints excluded: chain N residue 221 ASP Chi-restraints excluded: chain N residue 296 THR Chi-restraints excluded: chain N residue 327 HIS Chi-restraints excluded: chain N residue 339 LEU Chi-restraints excluded: chain N residue 381 VAL Chi-restraints excluded: chain N residue 397 TYR Chi-restraints excluded: chain N residue 464 LEU Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 151 LEU Chi-restraints excluded: chain O residue 167 LEU Chi-restraints excluded: chain O residue 221 ASP Chi-restraints excluded: chain O residue 257 THR Chi-restraints excluded: chain O residue 296 THR Chi-restraints excluded: chain O residue 327 HIS Chi-restraints excluded: chain O residue 376 TYR Chi-restraints excluded: chain O residue 381 VAL Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain P residue 80 GLN Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 221 ASP Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 296 THR Chi-restraints excluded: chain P residue 327 HIS Chi-restraints excluded: chain P residue 376 TYR Chi-restraints excluded: chain P residue 381 VAL Chi-restraints excluded: chain P residue 473 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/iotbx/cli_parser.py", line 939, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.4492 > 50: distance: 1 - 21: 3.433 distance: 8 - 29: 4.668 distance: 12 - 36: 8.988 distance: 17 - 21: 3.062 distance: 18 - 44: 14.049 distance: 23 - 24: 8.231 distance: 24 - 56: 9.915 distance: 25 - 26: 6.286 distance: 26 - 27: 6.946 distance: 26 - 28: 15.605 distance: 29 - 30: 5.377 distance: 30 - 31: 3.799 distance: 30 - 33: 4.273 distance: 31 - 32: 3.851 distance: 32 - 62: 22.385 distance: 33 - 34: 5.764 distance: 33 - 35: 5.790 distance: 36 - 37: 6.121 distance: 37 - 38: 10.537 distance: 37 - 40: 13.966 distance: 38 - 39: 3.103 distance: 38 - 44: 12.918 distance: 39 - 67: 28.194 distance: 40 - 41: 10.881 distance: 40 - 42: 10.019 distance: 41 - 43: 12.928 distance: 44 - 45: 12.244 distance: 45 - 46: 8.165 distance: 45 - 48: 9.575 distance: 46 - 47: 7.388 distance: 46 - 56: 11.148 distance: 47 - 81: 6.473 distance: 48 - 49: 3.607 distance: 49 - 50: 5.362 distance: 49 - 51: 4.360 distance: 50 - 52: 4.077 distance: 51 - 53: 5.142 distance: 52 - 54: 4.503 distance: 53 - 54: 4.538 distance: 54 - 55: 4.507 distance: 56 - 57: 10.135 distance: 57 - 58: 24.477 distance: 57 - 60: 18.213 distance: 58 - 59: 19.826 distance: 58 - 62: 26.981 distance: 59 - 89: 20.745 distance: 62 - 63: 17.211 distance: 63 - 64: 11.078 distance: 63 - 66: 23.754 distance: 64 - 65: 23.525 distance: 64 - 67: 18.768 distance: 67 - 68: 7.044 distance: 68 - 69: 19.144 distance: 68 - 71: 7.685 distance: 69 - 70: 8.594 distance: 69 - 81: 5.301 distance: 71 - 72: 13.223 distance: 72 - 73: 7.693 distance: 72 - 74: 7.342 distance: 73 - 75: 10.126 distance: 74 - 76: 14.622 distance: 74 - 77: 7.125 distance: 75 - 76: 9.683 distance: 76 - 78: 6.375 distance: 77 - 79: 9.473 distance: 78 - 80: 9.192 distance: 79 - 80: 10.681 distance: 82 - 85: 3.280 distance: 83 - 89: 3.800 distance: 85 - 86: 6.286 distance: 85 - 87: 6.306 distance: 86 - 88: 13.732 distance: 89 - 90: 3.736 distance: 90 - 91: 11.843 distance: 90 - 93: 6.008 distance: 91 - 92: 8.769 distance: 91 - 95: 10.970 distance: 92 - 119: 12.021 distance: 93 - 94: 7.658 distance: 95 - 96: 7.827 distance: 96 - 99: 5.140 distance: 97 - 98: 4.279 distance: 98 - 126: 5.742 distance: 99 - 100: 10.040 distance: 100 - 101: 6.075