Starting phenix.real_space_refine on Sat Jan 20 07:22:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/01_2024/6v1x_21018_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/01_2024/6v1x_21018.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/01_2024/6v1x_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_21018/01_2024/6v1x_21018_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/01_2024/6v1x_21018_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/01_2024/6v1x_21018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/01_2024/6v1x_21018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/01_2024/6v1x_21018_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1x_21018/01_2024/6v1x_21018_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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. 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" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: {'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} Time building chain proxies: 7.49, per 1000 atoms: 0.54 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: 5.60 Conformation dependent library (CDL) restraints added in 2.4 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: 2.82 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: 3.45 Time building geometry restraints manager: 5.98 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=" 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 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 bond pdb=" C PRO A 150 " pdb=" N LEU A 151 " ideal model delta sigma weight residual 1.334 1.497 -0.163 1.46e-02 4.69e+03 1.24e+02 bond pdb=" C3 QNJ B 602 " pdb=" O1 QNJ B 602 " ideal model delta sigma weight residual 1.416 1.336 0.080 2.00e-02 2.50e+03 1.59e+01 ... (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 - 21.91: 8192 21.91 - 43.82: 252 43.82 - 65.72: 16 65.72 - 87.63: 12 87.63 - 109.54: 4 Dihedral angle restraints: 8476 sinusoidal: 3184 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 8473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1889 0.084 - 0.167: 315 0.167 - 0.251: 40 0.251 - 0.334: 16 0.334 - 0.418: 4 Chirality restraints: 2264 Sorted by residual: 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 chirality pdb=" C10 QNJ C 601 " pdb=" C1 QNJ C 601 " pdb=" C5 QNJ C 601 " pdb=" C9 QNJ C 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 chirality pdb=" C10 QNJ A 602 " pdb=" C1 QNJ A 602 " pdb=" C5 QNJ A 602 " pdb=" C9 QNJ A 602 " 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 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 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: 1.700 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: 8.410 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 37.650 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.070 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5818 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 14408 Z= 0.707 Angle : 1.193 10.087 19696 Z= 0.653 Chirality : 0.069 0.418 2264 Planarity : 0.008 0.059 2416 Dihedral : 11.742 109.541 5044 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.50 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 75 HIS 0.014 0.003 HIS C 301 PHE 0.025 0.003 PHE B 92 TYR 0.035 0.003 TYR A 223 ARG 0.005 0.001 ARG D 322 *********************** 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 : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8537 (mt0) cc_final: 0.8210 (mt0) REVERT: A 270 ASN cc_start: 0.8109 (t0) cc_final: 0.7808 (t0) REVERT: B 96 ASN cc_start: 0.9089 (m-40) cc_final: 0.8855 (m110) REVERT: B 149 GLN cc_start: 0.8598 (mt0) cc_final: 0.8049 (mt0) REVERT: B 270 ASN cc_start: 0.8039 (t0) cc_final: 0.7778 (t0) REVERT: C 105 ASP cc_start: 0.7856 (t0) cc_final: 0.7654 (t0) REVERT: C 149 GLN cc_start: 0.8538 (mt0) cc_final: 0.8218 (mt0) REVERT: C 270 ASN cc_start: 0.8114 (t0) cc_final: 0.7805 (t0) REVERT: D 149 GLN cc_start: 0.8539 (mt0) cc_final: 0.8219 (mt0) REVERT: D 270 ASN cc_start: 0.8110 (t0) cc_final: 0.7810 (t0) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.3062 time to fit residues: 144.0584 Evaluate side-chains 209 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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: 0.8980 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 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: 0.4980 chunk 159 optimal weight: 0.0050 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 284 ASN B 354 ASN C 284 ASN C 354 ASN D 284 ASN D 354 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5809 moved from start: 0.2844 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= 0.158 Angle : 0.588 5.381 19696 Z= 0.311 Chirality : 0.041 0.131 2264 Planarity : 0.004 0.035 2416 Dihedral : 9.671 108.765 2312 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.24 % Favored : 92.53 % Rotamer: Outliers : 2.25 % Allowed : 8.16 % Favored : 89.60 % 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: -1.68 (0.19), residues: 1768 helix: -0.09 (0.15), residues: 1040 sheet: -2.22 (0.50), residues: 96 loop : -2.65 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 253 HIS 0.002 0.001 HIS C 336 PHE 0.033 0.001 PHE B 92 TYR 0.021 0.002 TYR D 376 ARG 0.002 0.000 ARG A 272 *********************** 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 264 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 234 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7389 (ttm-80) REVERT: C 314 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7390 (ttm-80) REVERT: D 314 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7400 (ttm-80) outliers start: 30 outliers final: 15 residues processed: 253 average time/residue: 0.2566 time to fit residues: 95.6688 Evaluate side-chains 205 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 133 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 158 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5870 moved from start: 0.3393 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= 0.181 Angle : 0.539 5.379 19696 Z= 0.285 Chirality : 0.041 0.133 2264 Planarity : 0.004 0.033 2416 Dihedral : 8.682 103.730 2312 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.01 % Favored : 92.76 % Rotamer: Outliers : 2.40 % Allowed : 10.85 % Favored : 86.75 % 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: -0.58 (0.21), residues: 1768 helix: 0.96 (0.16), residues: 1044 sheet: -1.96 (0.52), residues: 96 loop : -2.51 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 253 HIS 0.003 0.001 HIS B 336 PHE 0.027 0.001 PHE A 155 TYR 0.017 0.001 TYR D 133 ARG 0.002 0.000 ARG D 197 *********************** 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 241 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 209 time to evaluate : 1.478 Fit side-chains REVERT: A 195 TRP cc_start: 0.6234 (m100) cc_final: 0.6006 (m100) REVERT: A 314 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7453 (ttm-80) REVERT: C 195 TRP cc_start: 0.6202 (m100) cc_final: 0.5990 (m100) REVERT: C 314 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7455 (ttm-80) REVERT: D 314 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7447 (ttm-80) outliers start: 32 outliers final: 17 residues processed: 226 average time/residue: 0.2583 time to fit residues: 84.9901 Evaluate side-chains 212 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 83 optimal weight: 50.0000 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 170 optimal weight: 9.9990 chunk 152 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN B 149 GLN B 354 ASN C 354 ASN D 354 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14408 Z= 0.245 Angle : 0.561 6.005 19696 Z= 0.296 Chirality : 0.043 0.144 2264 Planarity : 0.004 0.034 2416 Dihedral : 8.266 96.886 2312 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.13 % Favored : 92.42 % Rotamer: Outliers : 3.07 % Allowed : 11.15 % Favored : 85.78 % 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: -0.22 (0.21), residues: 1768 helix: 1.26 (0.17), residues: 1044 sheet: -2.00 (0.51), residues: 96 loop : -2.33 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 253 HIS 0.006 0.001 HIS A 336 PHE 0.031 0.001 PHE A 155 TYR 0.015 0.002 TYR A 252 ARG 0.002 0.000 ARG D 184 *********************** 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 250 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 209 time to evaluate : 1.526 Fit side-chains outliers start: 41 outliers final: 28 residues processed: 228 average time/residue: 0.2668 time to fit residues: 87.8970 Evaluate side-chains 222 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 397 TYR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 126 optimal weight: 0.0470 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 30.0000 chunk 152 optimal weight: 0.0970 chunk 42 optimal weight: 50.0000 chunk 57 optimal weight: 1.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 348 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.4215 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 : 0.487 5.253 19696 Z= 0.256 Chirality : 0.041 0.143 2264 Planarity : 0.003 0.031 2416 Dihedral : 7.529 85.171 2312 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.22 % Favored : 93.38 % Rotamer: Outliers : 1.72 % Allowed : 14.52 % Favored : 83.76 % 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: 0.26 (0.21), residues: 1768 helix: 1.65 (0.17), residues: 1036 sheet: -1.74 (0.51), residues: 96 loop : -2.11 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 253 HIS 0.002 0.001 HIS B 336 PHE 0.028 0.001 PHE D 155 TYR 0.015 0.001 TYR D 133 ARG 0.004 0.000 ARG B 222 *********************** 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 245 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 222 time to evaluate : 1.410 Fit side-chains REVERT: A 105 ASP cc_start: 0.7756 (t0) cc_final: 0.7556 (t0) outliers start: 23 outliers final: 19 residues processed: 235 average time/residue: 0.2128 time to fit residues: 76.9690 Evaluate side-chains 222 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 397 TYR 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: 20.0000 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.0970 chunk 170 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5962 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14408 Z= 0.255 Angle : 0.559 6.576 19696 Z= 0.292 Chirality : 0.043 0.156 2264 Planarity : 0.003 0.036 2416 Dihedral : 7.986 87.057 2312 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.30 % Favored : 92.36 % Rotamer: Outliers : 3.82 % Allowed : 13.70 % Favored : 82.49 % 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: 0.13 (0.21), residues: 1768 helix: 1.46 (0.17), residues: 1044 sheet: -2.01 (0.47), residues: 116 loop : -1.95 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 253 HIS 0.006 0.001 HIS B 336 PHE 0.034 0.001 PHE B 92 TYR 0.016 0.001 TYR D 252 ARG 0.002 0.000 ARG B 222 *********************** 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 261 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 1.596 Fit side-chains REVERT: A 105 ASP cc_start: 0.8143 (t0) cc_final: 0.7891 (t0) REVERT: B 105 ASP cc_start: 0.7691 (t0) cc_final: 0.7487 (t0) outliers start: 51 outliers final: 34 residues processed: 237 average time/residue: 0.2194 time to fit residues: 80.4452 Evaluate side-chains 242 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 397 TYR Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 0.5980 chunk 97 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 96 optimal weight: 0.0070 chunk 143 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 106 optimal weight: 0.0370 chunk 103 optimal weight: 0.9990 chunk 78 optimal weight: 0.4980 chunk 104 optimal weight: 0.0670 overall best weight: 0.1414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS B 149 GLN B 336 HIS D 336 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5841 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14408 Z= 0.116 Angle : 0.488 7.964 19696 Z= 0.251 Chirality : 0.040 0.148 2264 Planarity : 0.003 0.038 2416 Dihedral : 7.278 75.570 2312 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.60 % Favored : 94.17 % Rotamer: Outliers : 2.17 % Allowed : 16.32 % Favored : 81.51 % 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: 0.56 (0.22), residues: 1768 helix: 1.85 (0.17), residues: 1032 sheet: -1.93 (0.47), residues: 116 loop : -1.79 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 253 HIS 0.001 0.000 HIS B 267 PHE 0.035 0.001 PHE B 92 TYR 0.009 0.001 TYR A 217 ARG 0.003 0.000 ARG B 222 *********************** 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 245 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 1.531 Fit side-chains REVERT: D 105 ASP cc_start: 0.7950 (t0) cc_final: 0.7683 (t0) outliers start: 29 outliers final: 15 residues processed: 234 average time/residue: 0.1995 time to fit residues: 74.7684 Evaluate side-chains 212 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 397 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 32 optimal weight: 40.0000 chunk 107 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 83 optimal weight: 50.0000 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN B 455 GLN D 149 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.4806 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= 0.166 Angle : 0.514 8.684 19696 Z= 0.264 Chirality : 0.042 0.146 2264 Planarity : 0.003 0.042 2416 Dihedral : 7.514 77.953 2312 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.79 % Favored : 92.99 % Rotamer: Outliers : 2.92 % Allowed : 15.42 % Favored : 81.66 % 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: 0.48 (0.22), residues: 1768 helix: 1.79 (0.17), residues: 1032 sheet: -1.81 (0.48), residues: 116 loop : -1.86 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 230 HIS 0.004 0.001 HIS C 336 PHE 0.025 0.001 PHE D 155 TYR 0.010 0.001 TYR D 252 ARG 0.003 0.000 ARG B 222 *********************** 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 249 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 1.529 Fit side-chains REVERT: B 170 LEU cc_start: 0.9293 (mt) cc_final: 0.9070 (tt) outliers start: 39 outliers final: 28 residues processed: 231 average time/residue: 0.2183 time to fit residues: 78.4976 Evaluate side-chains 233 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 205 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TYR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 73 SER Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 381 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 149 optimal weight: 0.0470 chunk 157 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.4938 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= 0.169 Angle : 0.525 9.759 19696 Z= 0.268 Chirality : 0.042 0.150 2264 Planarity : 0.003 0.043 2416 Dihedral : 7.348 75.183 2312 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.83 % Favored : 93.95 % Rotamer: Outliers : 2.47 % Allowed : 15.87 % Favored : 81.66 % 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: 0.54 (0.22), residues: 1768 helix: 1.84 (0.17), residues: 1028 sheet: -1.17 (0.56), residues: 96 loop : -1.94 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 137 HIS 0.003 0.001 HIS C 118 PHE 0.024 0.001 PHE C 155 TYR 0.020 0.001 TYR D 133 ARG 0.002 0.000 ARG B 176 *********************** 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 240 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 1.511 Fit side-chains REVERT: B 170 LEU cc_start: 0.9260 (mt) cc_final: 0.9043 (tt) outliers start: 33 outliers final: 21 residues processed: 226 average time/residue: 0.2137 time to fit residues: 74.0467 Evaluate side-chains 224 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 327 HIS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 327 HIS Chi-restraints excluded: chain D residue 339 LEU 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: 0.0670 chunk 79 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 0.0270 chunk 107 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN B 149 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5853 moved from start: 0.5190 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= 0.123 Angle : 0.509 11.219 19696 Z= 0.256 Chirality : 0.041 0.151 2264 Planarity : 0.003 0.043 2416 Dihedral : 6.757 69.576 2312 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.77 % Favored : 94.00 % Rotamer: Outliers : 1.35 % Allowed : 17.22 % Favored : 81.44 % 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: 0.83 (0.22), residues: 1768 helix: 2.08 (0.17), residues: 1024 sheet: -1.12 (0.56), residues: 96 loop : -1.81 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 253 HIS 0.002 0.001 HIS C 118 PHE 0.023 0.001 PHE A 155 TYR 0.015 0.001 TYR D 86 ARG 0.002 0.000 ARG B 222 ********************** 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 220 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 202 time to evaluate : 1.553 Fit side-chains REVERT: B 80 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8674 (pp30) outliers start: 18 outliers final: 14 residues processed: 209 average time/residue: 0.2060 time to fit residues: 68.7587 Evaluate side-chains 210 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 265 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 143 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.195546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136132 restraints weight = 21882.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.130273 restraints weight = 13604.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.132547 restraints weight = 12806.035| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14408 Z= 0.248 Angle : 0.568 10.839 19696 Z= 0.287 Chirality : 0.043 0.151 2264 Planarity : 0.003 0.046 2416 Dihedral : 6.896 68.731 2312 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.28 % Favored : 93.50 % Rotamer: Outliers : 2.47 % Allowed : 16.99 % Favored : 80.54 % 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: 0.54 (0.21), residues: 1768 helix: 1.79 (0.16), residues: 1032 sheet: -1.13 (0.57), residues: 96 loop : -1.88 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 230 HIS 0.005 0.001 HIS C 336 PHE 0.023 0.001 PHE C 155 TYR 0.015 0.001 TYR C 86 ARG 0.003 0.000 ARG B 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2690.95 seconds wall clock time: 49 minutes 39.59 seconds (2979.59 seconds total)