Starting phenix.real_space_refine on Sun Nov 17 15:25:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcq_37446/11_2024/8wcq_37446.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcq_37446/11_2024/8wcq_37446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcq_37446/11_2024/8wcq_37446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcq_37446/11_2024/8wcq_37446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcq_37446/11_2024/8wcq_37446.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wcq_37446/11_2024/8wcq_37446.cif" } resolution = 3.35 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= 0.001 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: 6 Type Number sf(0) Gaussians P 35 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 9455 2.51 5 N 2065 2.21 5 O 2550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14130 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "E" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "B" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "C" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "D" Number of atoms: 2537 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2588 Chain: "A" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 289 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PEE:plan-1': 1, 'PEE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 15.69, per 1000 atoms: 1.11 Number of scatterers: 14130 At special positions: 0 Unit cell: (92.72, 92.72, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 20 16.00 P 35 15.00 O 2550 8.00 N 2065 7.00 C 9455 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 - 3.00 Amino acid : True - 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: 4.65 Conformation dependent library (CDL) restraints added in 3.2 seconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 38.1% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 50 through 53 Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 194 through 198 removed outlier: 3.756A pdb=" N TYR A 197 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.596A pdb=" N MET A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.710A pdb=" N SER A 218 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.519A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'E' and resid 50 through 53 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 194 through 198 removed outlier: 3.757A pdb=" N TYR E 197 " --> pdb=" O TYR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 213 removed outlier: 3.595A pdb=" N MET E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 218 removed outlier: 3.711A pdb=" N SER E 218 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.520A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 297 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing helix chain 'B' and resid 50 through 53 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 194 through 198 removed outlier: 3.757A pdb=" N TYR B 197 " --> pdb=" O TYR B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 213 removed outlier: 3.595A pdb=" N MET B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 218 removed outlier: 3.711A pdb=" N SER B 218 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.520A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'C' and resid 50 through 53 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 194 through 198 removed outlier: 3.756A pdb=" N TYR C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 213 removed outlier: 3.595A pdb=" N MET C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 218 removed outlier: 3.711A pdb=" N SER C 218 " --> pdb=" O ALA C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.521A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE C 297 " --> pdb=" O ARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 50 through 53 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 194 through 198 removed outlier: 3.756A pdb=" N TYR D 197 " --> pdb=" O TYR D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 213 removed outlier: 3.595A pdb=" N MET D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 218 removed outlier: 3.710A pdb=" N SER D 218 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 243 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.520A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 5.948A pdb=" N LEU A 16 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA A 143 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 18 " --> pdb=" O ALA A 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 94 removed outlier: 5.231A pdb=" N VAL A 89 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG A 105 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 91 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 108 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 38 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER A 29 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN A 40 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS A 27 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE A 42 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE A 25 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER A 44 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N TYR A 23 " --> pdb=" O SER A 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 78 removed outlier: 4.370A pdb=" N ASP A 185 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 164 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER A 191 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE A 162 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 16 through 20 removed outlier: 5.947A pdb=" N LEU E 16 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA E 143 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 18 " --> pdb=" O ALA E 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 88 through 94 removed outlier: 5.230A pdb=" N VAL E 89 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG E 105 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP E 91 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 108 " --> pdb=" O VAL E 39 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS E 38 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER E 29 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN E 40 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS E 27 " --> pdb=" O ASN E 40 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE E 42 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE E 25 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER E 44 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N TYR E 23 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 78 removed outlier: 4.369A pdb=" N ASP E 185 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 164 " --> pdb=" O ARG E 189 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER E 191 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE E 162 " --> pdb=" O SER E 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'B' and resid 16 through 20 removed outlier: 5.947A pdb=" N LEU B 16 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 143 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 18 " --> pdb=" O ALA B 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 94 removed outlier: 5.231A pdb=" N VAL B 89 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 105 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 91 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 108 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS B 38 " --> pdb=" O SER B 29 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER B 29 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ASN B 40 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N CYS B 27 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE B 42 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE B 25 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N SER B 44 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N TYR B 23 " --> pdb=" O SER B 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 78 removed outlier: 4.370A pdb=" N ASP B 185 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 164 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER B 191 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 162 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'C' and resid 16 through 20 removed outlier: 5.948A pdb=" N LEU C 16 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA C 143 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 18 " --> pdb=" O ALA C 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 88 through 94 removed outlier: 5.231A pdb=" N VAL C 89 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ARG C 105 " --> pdb=" O VAL C 89 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 91 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 108 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS C 38 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER C 29 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN C 40 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS C 27 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE C 42 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE C 25 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N SER C 44 " --> pdb=" O TYR C 23 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N TYR C 23 " --> pdb=" O SER C 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 77 through 78 removed outlier: 4.370A pdb=" N ASP C 185 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER C 164 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N SER C 191 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE C 162 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB8, first strand: chain 'D' and resid 16 through 20 removed outlier: 5.948A pdb=" N LEU D 16 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA D 143 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL D 18 " --> pdb=" O ALA D 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 88 through 94 removed outlier: 5.231A pdb=" N VAL D 89 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG D 105 " --> pdb=" O VAL D 89 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP D 91 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 108 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS D 38 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N SER D 29 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASN D 40 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N CYS D 27 " --> pdb=" O ASN D 40 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE D 42 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE D 25 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N SER D 44 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N TYR D 23 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.370A pdb=" N ASP D 185 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER D 164 " --> pdb=" O ARG D 189 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 191 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE D 162 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 77 through 78 655 hydrogen bonds defined for protein. 1840 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: 4.40 Time building geometry restraints manager: 5.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2182 1.32 - 1.44: 3753 1.44 - 1.57: 8390 1.57 - 1.69: 70 1.69 - 1.81: 35 Bond restraints: 14430 Sorted by residual: bond pdb=" CB AARG A 293 " pdb=" CG AARG A 293 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB AARG B 293 " pdb=" CG AARG B 293 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB AARG E 293 " pdb=" CG AARG E 293 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.34e+00 bond pdb=" CB AARG C 293 " pdb=" CG AARG C 293 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.34e+00 bond pdb=" CB AARG D 293 " pdb=" CG AARG D 293 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.33e+00 ... (remaining 14425 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 18571 1.08 - 2.16: 624 2.16 - 3.24: 140 3.24 - 4.32: 30 4.32 - 5.40: 20 Bond angle restraints: 19385 Sorted by residual: angle pdb=" CA LYS C 248 " pdb=" CB LYS C 248 " pdb=" CG LYS C 248 " ideal model delta sigma weight residual 114.10 119.25 -5.15 2.00e+00 2.50e-01 6.62e+00 angle pdb=" CA LYS A 248 " pdb=" CB LYS A 248 " pdb=" CG LYS A 248 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA LYS E 248 " pdb=" CB LYS E 248 " pdb=" CG LYS E 248 " ideal model delta sigma weight residual 114.10 119.24 -5.14 2.00e+00 2.50e-01 6.60e+00 angle pdb=" CA LYS B 248 " pdb=" CB LYS B 248 " pdb=" CG LYS B 248 " ideal model delta sigma weight residual 114.10 119.23 -5.13 2.00e+00 2.50e-01 6.58e+00 angle pdb=" CA LYS D 248 " pdb=" CB LYS D 248 " pdb=" CG LYS D 248 " ideal model delta sigma weight residual 114.10 119.20 -5.10 2.00e+00 2.50e-01 6.50e+00 ... (remaining 19380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 8599 34.73 - 69.46: 256 69.46 - 104.18: 60 104.18 - 138.91: 35 138.91 - 173.64: 20 Dihedral angle restraints: 8970 sinusoidal: 4270 harmonic: 4700 Sorted by residual: dihedral pdb=" C4 PEE D 401 " pdb=" O4P PEE D 401 " pdb=" P PEE D 401 " pdb=" O1P PEE D 401 " ideal model delta sinusoidal sigma weight residual 57.28 -129.08 -173.64 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE B 401 " pdb=" O4P PEE B 401 " pdb=" P PEE B 401 " pdb=" O1P PEE B 401 " ideal model delta sinusoidal sigma weight residual 57.28 -129.11 -173.61 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C4 PEE E 409 " pdb=" O4P PEE E 409 " pdb=" P PEE E 409 " pdb=" O1P PEE E 409 " ideal model delta sinusoidal sigma weight residual 57.28 -129.13 -173.59 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 8967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1211 0.028 - 0.055: 501 0.055 - 0.083: 215 0.083 - 0.111: 148 0.111 - 0.139: 40 Chirality restraints: 2115 Sorted by residual: chirality pdb=" CA ILE D 92 " pdb=" N ILE D 92 " pdb=" C ILE D 92 " pdb=" CB ILE D 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA ILE E 92 " pdb=" N ILE E 92 " pdb=" C ILE E 92 " pdb=" CB ILE E 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 2112 not shown) Planarity restraints: 2305 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 246 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO A 247 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 246 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO D 247 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 247 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 247 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 246 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.79e+00 pdb=" N PRO B 247 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " -0.033 5.00e-02 4.00e+02 ... (remaining 2302 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3413 2.80 - 3.33: 12175 3.33 - 3.85: 21216 3.85 - 4.38: 24927 4.38 - 4.90: 46028 Nonbonded interactions: 107759 Sorted by model distance: nonbonded pdb=" OG1 THR B 20 " pdb=" O ALA B 143 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR D 20 " pdb=" O ALA D 143 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR A 20 " pdb=" O ALA A 143 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR E 20 " pdb=" O ALA E 143 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR C 20 " pdb=" O ALA C 143 " model vdw 2.279 3.040 ... (remaining 107754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )) or (resid 404 through 405 and (name N \ or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or nam \ e C30 or name C31 or name C32 or name C33 or name C4 or name C5 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or resid 406 or (resid 407 and (name C1 or name C10 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name \ O4P or name O5 or name P )) or (resid 408 through 409 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or resid 403 or (re \ sid 404 through 405 and (name N or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C \ 19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )) or (resid 406 and (name N or name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or \ name O5 or name P )) or (resid 407 and (name C1 or name C10 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name \ O4P or name O5 or name P )) or (resid 408 through 409 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or resid 403 or (re \ sid 404 through 405 and (name N or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C \ 19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )) or (resid 406 and (name N or name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or \ name O5 or name P )) or (resid 407 and (name C1 or name C10 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name \ O4P or name O5 or name P )) or (resid 408 through 409 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or resid 403 or (re \ sid 404 through 405 and (name N or name C1 or name C10 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C \ 19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C4 or name C5 or name O1P or name O2 or name O2P or name O3 or name O3P or name \ O4 or name O4P or name O5 or name P )) or (resid 406 and (name N or name C1 or \ name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 \ or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or na \ me C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or \ name O5 or name P )) or (resid 407 and (name C1 or name C10 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name \ O4P or name O5 or name P )) or (resid 408 through 409 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 403 and ( \ name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 \ or name C16 or name C17 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or nam \ e C39 or name C40 or name O1P or name O2 or name O2P or name O3 or name O3P or n \ ame O4 or name O4P or name O5 or name P )) or (resid 404 through 405 and (name N \ or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name \ C15 or name C16 or name C17 or name C18 or name C19 or name C2 or name C3 or nam \ e C30 or name C31 or name C32 or name C33 or name C4 or name C5 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or resid 406 or (resid 407 and (name C1 or name C10 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or \ name C19 or name C2 or name C20 or name C21 or name C3 or name C30 or name C31 o \ r name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C \ 38 or name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name \ O4P or name O5 or name P )) or (resid 408 through 409 and (name C10 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name \ C18 or name C19 or name C20 or name C21 or name C22)))) } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 44.400 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 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 : 0.003 0.056 14430 Z= 0.194 Angle : 0.522 5.402 19385 Z= 0.277 Chirality : 0.043 0.139 2115 Planarity : 0.005 0.060 2305 Dihedral : 22.283 173.642 5910 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % 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: 0.24 (0.22), residues: 1555 helix: 2.51 (0.23), residues: 500 sheet: -0.46 (0.27), residues: 445 loop : -1.38 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 72 HIS 0.002 0.001 HIS E 277 PHE 0.023 0.001 PHE B 37 TYR 0.007 0.001 TYR C 119 ARG 0.003 0.000 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.509 Fit side-chains REVERT: A 248 LYS cc_start: 0.6697 (tptt) cc_final: 0.6391 (mmtt) REVERT: E 23 TYR cc_start: 0.6433 (t80) cc_final: 0.6211 (t80) REVERT: E 248 LYS cc_start: 0.6755 (tptt) cc_final: 0.6513 (mmtt) REVERT: B 176 LEU cc_start: 0.8014 (tp) cc_final: 0.7802 (mt) REVERT: C 248 LYS cc_start: 0.6654 (tptt) cc_final: 0.6343 (mmmt) REVERT: D 248 LYS cc_start: 0.6795 (tptt) cc_final: 0.6493 (mmtt) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2441 time to fit residues: 114.5825 Evaluate side-chains 171 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 0.0010 chunk 140 optimal weight: 5.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 ASN B 307 ASN C 307 ASN D 307 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 14430 Z= 0.470 Angle : 0.914 8.891 19385 Z= 0.455 Chirality : 0.056 0.179 2115 Planarity : 0.008 0.063 2305 Dihedral : 23.983 176.229 2965 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.92 % Allowed : 14.16 % Favored : 82.92 % 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: -0.29 (0.21), residues: 1555 helix: 1.88 (0.21), residues: 500 sheet: -0.22 (0.29), residues: 405 loop : -1.89 (0.21), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.006 TRP D 72 HIS 0.005 0.002 HIS A 235 PHE 0.032 0.003 PHE E 78 TYR 0.020 0.002 TYR A 254 ARG 0.009 0.002 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 142 time to evaluate : 1.485 Fit side-chains REVERT: E 307 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8676 (m-40) REVERT: B 307 ASN cc_start: 0.8942 (OUTLIER) cc_final: 0.8728 (m-40) REVERT: C 307 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (m-40) REVERT: D 109 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7562 (ttm110) REVERT: D 307 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8597 (m-40) outliers start: 41 outliers final: 16 residues processed: 172 average time/residue: 0.2747 time to fit residues: 69.5030 Evaluate side-chains 123 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 109 ARG Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 307 ASN Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 307 ASN Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 307 ASN Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 307 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.6321 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: