Starting phenix.real_space_refine (version: dev) on Tue Apr 5 14:23:34 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/04_2022/6v1x_21018_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 13996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3436 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 174 Chain: "B" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3436 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 174 Chain: "C" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3436 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 174 Chain: "D" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3436 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 258 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 174 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'QNP': 1, 'QNJ': 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: {'QNP': 1, 'QNJ': 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: {'QNP': 1, 'QNJ': 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: {'QNP': 1, 'QNJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.14, per 1000 atoms: 0.58 Number of scatterers: 13996 At special positions: 0 Unit cell: (115.976, 115.976, 120.232, 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 64 16.00 P 4 15.00 O 2348 8.00 N 2276 7.00 C 9304 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: 5.88 Conformation dependent library (CDL) restraints added in 2.1 seconds 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 0 sheets defined 58.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 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 497 640 hydrogen bonds defined for protein. 1920 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: 3.21 Time building geometry restraints manager: 6.29 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: 2024 1.29 - 1.42: 4252 1.42 - 1.55: 8002 1.55 - 1.68: 26 1.68 - 1.81: 104 Bond restraints: 14408 Sorted by residual: bond pdb=" C17 QNJ D 601 " pdb=" C20 QNJ D 601 " ideal model delta sigma weight residual 1.360 1.596 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C17 QNJ C 601 " pdb=" C20 QNJ C 601 " ideal model delta sigma weight residual 1.360 1.596 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C17 QNJ A 602 " pdb=" C20 QNJ A 602 " ideal model delta sigma weight residual 1.360 1.596 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C17 QNJ B 602 " pdb=" C20 QNJ B 602 " ideal model delta sigma weight residual 1.360 1.596 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C11 QNJ C 601 " pdb=" C12 QNJ C 601 " ideal model delta sigma weight residual 1.682 1.453 0.229 2.00e-02 2.50e+03 1.31e+02 ... (remaining 14403 not shown) Histogram of bond angle deviations from ideal: 95.24 - 103.00: 131 103.00 - 110.76: 4749 110.76 - 118.52: 6293 118.52 - 126.29: 8235 126.29 - 134.05: 288 Bond angle restraints: 19696 Sorted by residual: 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 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 angle pdb=" C THR C 259 " pdb=" N THR C 260 " pdb=" CA THR C 260 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C THR D 259 " pdb=" N THR D 260 " pdb=" CA THR D 260 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C LYS B 127 " pdb=" N LYS B 128 " pdb=" CA LYS B 128 " ideal model delta sigma weight residual 121.54 129.82 -8.28 1.91e+00 2.74e-01 1.88e+01 ... (remaining 19691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 8044 23.98 - 47.96: 160 47.96 - 71.94: 12 71.94 - 95.92: 4 95.92 - 119.90: 8 Dihedral angle restraints: 8228 sinusoidal: 2936 harmonic: 5292 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 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 dihedral pdb=" CA SER A 125 " pdb=" C SER A 125 " pdb=" N PRO A 126 " pdb=" CA PRO A 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 8225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 2060 0.106 - 0.213: 171 0.213 - 0.319: 25 0.319 - 0.425: 0 0.425 - 0.531: 8 Chirality restraints: 2264 Sorted by residual: chirality pdb=" C5 QNJ C 601 " pdb=" C10 QNJ C 601 " pdb=" C4 QNJ C 601 " pdb=" C6 QNJ C 601 " both_signs ideal model delta sigma weight residual False -2.69 -2.16 -0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" C5 QNJ D 601 " pdb=" C10 QNJ D 601 " pdb=" C4 QNJ D 601 " pdb=" C6 QNJ D 601 " both_signs ideal model delta sigma weight residual False -2.69 -2.16 -0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" C5 QNJ B 602 " pdb=" C10 QNJ B 602 " pdb=" C4 QNJ B 602 " pdb=" C6 QNJ B 602 " both_signs ideal model delta sigma weight residual False -2.69 -2.16 -0.53 2.00e-01 2.50e+01 7.06e+00 ... (remaining 2261 not shown) Planarity restraints: 2416 Sorted by residual: 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 C 439 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C VAL C 439 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL C 439 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE C 440 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 439 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C VAL A 439 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL A 439 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE A 440 " -0.018 2.00e-02 2.50e+03 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3886 2.80 - 3.33: 12986 3.33 - 3.85: 21794 3.85 - 4.38: 23538 4.38 - 4.90: 41257 Nonbonded interactions: 103461 Sorted by model distance: nonbonded pdb=" O ALA B 358 " pdb=" OG SER B 361 " model vdw 2.279 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 nonbonded pdb=" O ALA A 358 " pdb=" OG SER A 361 " model vdw 2.280 2.440 nonbonded pdb=" O PHE A 191 " pdb=" NH2 ARG B 310 " model vdw 2.312 2.520 ... (remaining 103456 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) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 64 5.16 5 C 9304 2.51 5 N 2276 2.21 5 O 2348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.960 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: 9.040 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.110 Process input model: 37.900 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 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 : 0.013 0.236 14408 Z= 0.881 Angle : 1.225 10.087 19696 Z= 0.660 Chirality : 0.072 0.531 2264 Planarity : 0.008 0.059 2416 Dihedral : 11.531 119.902 4796 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.50 % Favored : 90.27 % Rotamer Outliers : 0.00 % 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: -3.79 (0.16), residues: 1768 helix: -2.08 (0.12), residues: 1000 sheet: -2.22 (0.52), residues: 96 loop : -3.08 (0.22), residues: 672 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 343 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.2901 time to fit residues: 137.8175 Evaluate side-chains 204 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 159 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 354 ASN B 96 ASN B 284 ASN B 354 ASN C 284 ASN C 354 ASN D 284 ASN D 354 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5936 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14408 Z= 0.175 Angle : 0.629 7.067 19696 Z= 0.323 Chirality : 0.043 0.197 2264 Planarity : 0.004 0.035 2416 Dihedral : 9.941 102.208 2064 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.24 % Favored : 92.53 % Rotamer Outliers : 1.95 % 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: -1.69 (0.19), residues: 1768 helix: -0.13 (0.15), residues: 1044 sheet: -2.20 (0.50), residues: 96 loop : -2.61 (0.24), residues: 628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 1.459 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 236 average time/residue: 0.2258 time to fit residues: 81.5337 Evaluate side-chains 195 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1315 time to fit residues: 4.5590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 0.0980 chunk 158 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN C 149 GLN D 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 14408 Z= 0.244 Angle : 0.616 6.096 19696 Z= 0.316 Chirality : 0.044 0.140 2264 Planarity : 0.004 0.035 2416 Dihedral : 9.739 101.941 2064 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.13 % Favored : 92.42 % Rotamer Outliers : 1.80 % 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: -0.74 (0.20), residues: 1768 helix: 0.79 (0.16), residues: 1044 sheet: -2.02 (0.52), residues: 96 loop : -2.49 (0.24), residues: 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 220 time to evaluate : 1.664 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 233 average time/residue: 0.2271 time to fit residues: 80.3446 Evaluate side-chains 221 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1206 time to fit residues: 6.2314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.9990 chunk 120 optimal weight: 50.0000 chunk 83 optimal weight: 50.0000 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 50.0000 chunk 107 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 170 optimal weight: 40.0000 chunk 152 optimal weight: 0.1980 chunk 45 optimal weight: 0.0970 chunk 141 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 354 ASN B 149 GLN B 354 ASN C 149 GLN C 354 ASN D 149 GLN D 354 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 14408 Z= 0.149 Angle : 0.534 6.081 19696 Z= 0.272 Chirality : 0.042 0.138 2264 Planarity : 0.003 0.035 2416 Dihedral : 9.336 99.343 2064 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.28 % Favored : 93.27 % Rotamer Outliers : 1.65 % 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: -0.10 (0.21), residues: 1768 helix: 1.36 (0.17), residues: 1040 sheet: -1.92 (0.50), residues: 96 loop : -2.29 (0.25), residues: 632 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 233 time to evaluate : 1.612 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 249 average time/residue: 0.2398 time to fit residues: 88.4745 Evaluate side-chains 220 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1183 time to fit residues: 5.1825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 126 optimal weight: 0.0870 chunk 70 optimal weight: 0.9990 chunk 145 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 50.0000 chunk 152 optimal weight: 0.9980 chunk 42 optimal weight: 50.0000 chunk 57 optimal weight: 2.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN B 348 GLN C 149 GLN C 348 GLN D 149 GLN D 348 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 14408 Z= 0.157 Angle : 0.515 5.602 19696 Z= 0.266 Chirality : 0.042 0.139 2264 Planarity : 0.003 0.035 2416 Dihedral : 9.621 101.316 2064 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.39 % Favored : 93.38 % Rotamer Outliers : 1.12 % 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: 0.25 (0.21), residues: 1768 helix: 1.62 (0.17), residues: 1032 sheet: -1.65 (0.51), residues: 96 loop : -2.06 (0.25), residues: 640 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 211 time to evaluate : 2.049 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 218 average time/residue: 0.2279 time to fit residues: 76.3374 Evaluate side-chains 217 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 1.666 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1265 time to fit residues: 4.3544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 1.9990 chunk 33 optimal weight: 50.0000 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 170 optimal weight: 50.0000 chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 164 optimal weight: 50.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 327 HIS A 348 GLN B 149 GLN B 327 HIS C 327 HIS D 327 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 14408 Z= 0.179 Angle : 0.521 5.998 19696 Z= 0.267 Chirality : 0.042 0.167 2264 Planarity : 0.003 0.037 2416 Dihedral : 9.618 101.860 2064 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.28 % Favored : 93.50 % Rotamer Outliers : 2.99 % 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: 0.43 (0.22), residues: 1768 helix: 1.68 (0.17), residues: 1036 sheet: -1.36 (0.53), residues: 96 loop : -1.86 (0.26), residues: 636 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 219 time to evaluate : 1.749 Fit side-chains outliers start: 40 outliers final: 23 residues processed: 242 average time/residue: 0.2218 time to fit residues: 82.6118 Evaluate side-chains 225 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 1.647 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1342 time to fit residues: 7.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 143 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 chunk 103 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN D 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 14408 Z= 0.143 Angle : 0.508 6.601 19696 Z= 0.258 Chirality : 0.042 0.151 2264 Planarity : 0.003 0.038 2416 Dihedral : 9.394 101.885 2064 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.50 % Favored : 93.27 % Rotamer Outliers : 1.20 % 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: 0.55 (0.22), residues: 1768 helix: 1.82 (0.17), residues: 1032 sheet: -1.26 (0.54), residues: 96 loop : -1.92 (0.26), residues: 640 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 1.621 Fit side-chains outliers start: 16 outliers final: 3 residues processed: 228 average time/residue: 0.2215 time to fit residues: 78.4143 Evaluate side-chains 208 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 205 time to evaluate : 1.648 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1282 time to fit residues: 2.9530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 40.0000 chunk 32 optimal weight: 40.0000 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 50.0000 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN B 216 ASN D 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 14408 Z= 0.185 Angle : 0.543 9.605 19696 Z= 0.274 Chirality : 0.043 0.151 2264 Planarity : 0.003 0.039 2416 Dihedral : 9.456 102.797 2064 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.17 % Favored : 93.61 % Rotamer Outliers : 0.97 % 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 (0.22), residues: 1768 helix: 1.74 (0.17), residues: 1036 sheet: -1.22 (0.55), residues: 96 loop : -1.82 (0.26), residues: 636 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 208 time to evaluate : 1.688 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 211 average time/residue: 0.2214 time to fit residues: 72.2194 Evaluate side-chains 210 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 206 time to evaluate : 1.631 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1238 time to fit residues: 3.3014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 5.9990 chunk 148 optimal weight: 0.0470 chunk 158 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 149 optimal weight: 0.0030 chunk 157 optimal weight: 0.0370 chunk 103 optimal weight: 1.9990 overall best weight: 0.4968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN C 149 GLN D 336 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 14408 Z= 0.140 Angle : 0.536 11.768 19696 Z= 0.264 Chirality : 0.042 0.153 2264 Planarity : 0.003 0.038 2416 Dihedral : 9.223 101.423 2064 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.60 % Favored : 94.17 % Rotamer Outliers : 0.60 % 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: 0.71 (0.22), residues: 1768 helix: 1.86 (0.17), residues: 1036 sheet: -1.12 (0.56), residues: 96 loop : -1.70 (0.26), residues: 636 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 213 time to evaluate : 1.616 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 216 average time/residue: 0.2277 time to fit residues: 75.8392 Evaluate side-chains 209 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 203 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1330 time to fit residues: 3.7037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 20.0000 chunk 102 optimal weight: 0.0770 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 175 optimal weight: 40.0000 chunk 161 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN B 149 GLN C 149 GLN D 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6021 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14408 Z= 0.181 Angle : 0.551 11.736 19696 Z= 0.273 Chirality : 0.043 0.153 2264 Planarity : 0.003 0.040 2416 Dihedral : 9.284 102.679 2064 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.83 % Favored : 93.95 % Rotamer Outliers : 0.52 % 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: 0.62 (0.21), residues: 1768 helix: 1.80 (0.17), residues: 1036 sheet: -1.09 (0.56), residues: 96 loop : -1.77 (0.26), residues: 636 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 1.648 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 210 average time/residue: 0.2265 time to fit residues: 73.7676 Evaluate side-chains 206 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 202 time to evaluate : 1.691 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1309 time to fit residues: 3.4333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 0.0980 chunk 42 optimal weight: 50.0000 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 40.0000 chunk 139 optimal weight: 6.9990 chunk 58 optimal weight: 0.0270 chunk 143 optimal weight: 0.0050 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 overall best weight: 0.2252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 336 HIS B 149 GLN B 336 HIS C 149 GLN C 336 HIS D 149 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.197841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132277 restraints weight = 22061.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133380 restraints weight = 13122.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.133072 restraints weight = 9564.339| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 14408 Z= 0.120 Angle : 0.517 11.602 19696 Z= 0.254 Chirality : 0.041 0.152 2264 Planarity : 0.003 0.036 2416 Dihedral : 8.982 100.133 2064 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.60 % Favored : 94.17 % Rotamer Outliers : 0.15 % 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: 0.93 (0.22), residues: 1768 helix: 2.08 (0.17), residues: 1028 sheet: -0.98 (0.56), residues: 96 loop : -1.65 (0.26), residues: 644 =============================================================================== Job complete usr+sys time: 2579.00 seconds wall clock time: 47 minutes 36.62 seconds (2856.62 seconds total)