Starting phenix.real_space_refine (version: dev) on Mon Dec 12 14:53:26 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqu_13605/12_2022/7pqu_13605_updated.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10798 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "B" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "C" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "D" Number of atoms: 2671 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 328, 2661 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 312} Unresolved chain links: 1 Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 2725 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Unusual residues: {' K': 4, '805': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'805': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALYS A 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 449 " occ=0.50 residue: pdb=" N ALYS B 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 449 " occ=0.50 residue: pdb=" N ALYS C 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 449 " occ=0.50 residue: pdb=" N ALYS D 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS D 449 " occ=0.50 Time building chain proxies: 11.39, per 1000 atoms: 1.05 Number of scatterers: 10798 At special positions: 0 Unit cell: (100.04, 100.04, 115.62, 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) K 4 19.00 S 72 16.00 O 1842 8.00 N 1780 7.00 C 7100 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: 4.48 Conformation dependent library (CDL) restraints added in 2.8 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 4 sheets defined 55.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 removed outlier: 4.414A pdb=" N THR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.812A pdb=" N LEU A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 33 through 38' Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 64 through 70 removed outlier: 3.862A pdb=" N ASN A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 107 through 110 No H-bonds generated for 'chain 'A' and resid 107 through 110' Processing helix chain 'A' and resid 192 through 210 removed outlier: 4.544A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 261 removed outlier: 3.631A pdb=" N PHE A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 316 through 324 removed outlier: 3.895A pdb=" N ARG A 320 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 321 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 removed outlier: 3.582A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 369 removed outlier: 3.706A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 removed outlier: 3.847A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.906A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 450 removed outlier: 3.828A pdb=" N ASN A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 removed outlier: 4.414A pdb=" N THR B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.811A pdb=" N LEU B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 33 through 38' Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 64 through 70 removed outlier: 3.863A pdb=" N ASN B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 70 " --> pdb=" O HIS B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 192 through 210 removed outlier: 4.544A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 261 removed outlier: 3.631A pdb=" N PHE B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 311 through 314 No H-bonds generated for 'chain 'B' and resid 311 through 314' Processing helix chain 'B' and resid 316 through 324 removed outlier: 3.896A pdb=" N ARG B 320 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 321 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 removed outlier: 3.582A pdb=" N ARG B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 369 removed outlier: 3.706A pdb=" N LEU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 398 removed outlier: 3.847A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 429 removed outlier: 3.905A pdb=" N LEU B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 450 removed outlier: 3.827A pdb=" N ASN B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 28 removed outlier: 4.414A pdb=" N THR C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.812A pdb=" N LEU C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 38' Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 64 through 70 removed outlier: 3.862A pdb=" N ASN C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 107 through 110 No H-bonds generated for 'chain 'C' and resid 107 through 110' Processing helix chain 'C' and resid 192 through 210 removed outlier: 4.544A pdb=" N PHE C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 261 removed outlier: 3.631A pdb=" N PHE C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 311 through 314 No H-bonds generated for 'chain 'C' and resid 311 through 314' Processing helix chain 'C' and resid 316 through 324 removed outlier: 3.895A pdb=" N ARG C 320 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 321 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 removed outlier: 3.583A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 369 removed outlier: 3.706A pdb=" N LEU C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 398 removed outlier: 3.848A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 429 removed outlier: 3.906A pdb=" N LEU C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 450 removed outlier: 3.828A pdb=" N ASN C 438 " --> pdb=" O VAL C 434 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 4.414A pdb=" N THR D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 38 removed outlier: 3.811A pdb=" N LEU D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 33 through 38' Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 64 through 70 removed outlier: 3.862A pdb=" N ASN D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR D 70 " --> pdb=" O HIS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 107 through 110 No H-bonds generated for 'chain 'D' and resid 107 through 110' Processing helix chain 'D' and resid 192 through 210 removed outlier: 4.544A pdb=" N PHE D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 261 removed outlier: 3.631A pdb=" N PHE D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 311 through 314 No H-bonds generated for 'chain 'D' and resid 311 through 314' Processing helix chain 'D' and resid 316 through 324 removed outlier: 3.895A pdb=" N ARG D 320 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 321 " --> pdb=" O ILE D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.582A pdb=" N ARG D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 369 removed outlier: 3.706A pdb=" N LEU D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 398 removed outlier: 3.847A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 429 removed outlier: 3.906A pdb=" N LEU D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 450 removed outlier: 3.827A pdb=" N ASN D 438 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE D 439 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR A 17 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 14 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU A 54 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 47 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR B 17 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 14 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU B 54 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP B 47 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 17 through 22 removed outlier: 3.903A pdb=" N THR C 17 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 14 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU C 54 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP C 47 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 17 through 22 removed outlier: 3.904A pdb=" N THR D 17 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL D 14 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU D 54 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP D 47 " --> pdb=" O PHE D 56 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1316 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: 2.80 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1612 1.27 - 1.41: 3220 1.41 - 1.54: 6140 1.54 - 1.67: 16 1.67 - 1.81: 112 Bond restraints: 11100 Sorted by residual: bond pdb=" C GLY A 402 " pdb=" O GLY A 402 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.35e-02 5.49e+03 4.75e+01 bond pdb=" C GLY B 402 " pdb=" O GLY B 402 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.35e-02 5.49e+03 4.72e+01 bond pdb=" C GLY D 402 " pdb=" O GLY D 402 " ideal model delta sigma weight residual 1.235 1.142 0.093 1.35e-02 5.49e+03 4.70e+01 bond pdb=" C GLY C 402 " pdb=" O GLY C 402 " ideal model delta sigma weight residual 1.235 1.142 0.092 1.35e-02 5.49e+03 4.69e+01 bond pdb=" C13 805 B 601 " pdb=" C14 805 B 601 " ideal model delta sigma weight residual 1.346 1.438 -0.092 2.00e-02 2.50e+03 2.13e+01 ... (remaining 11095 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.66: 376 106.66 - 113.54: 5949 113.54 - 120.42: 4699 120.42 - 127.30: 3908 127.30 - 134.18: 172 Bond angle restraints: 15104 Sorted by residual: angle pdb=" N VAL D 264 " pdb=" CA VAL D 264 " pdb=" C VAL D 264 " ideal model delta sigma weight residual 113.71 107.57 6.14 9.50e-01 1.11e+00 4.17e+01 angle pdb=" N VAL A 264 " pdb=" CA VAL A 264 " pdb=" C VAL A 264 " ideal model delta sigma weight residual 113.71 107.61 6.10 9.50e-01 1.11e+00 4.13e+01 angle pdb=" N VAL C 264 " pdb=" CA VAL C 264 " pdb=" C VAL C 264 " ideal model delta sigma weight residual 113.71 107.62 6.09 9.50e-01 1.11e+00 4.11e+01 angle pdb=" N VAL B 264 " pdb=" CA VAL B 264 " pdb=" C VAL B 264 " ideal model delta sigma weight residual 113.71 107.63 6.08 9.50e-01 1.11e+00 4.09e+01 angle pdb=" C TRP A 94 " pdb=" N GLY A 95 " pdb=" CA GLY A 95 " ideal model delta sigma weight residual 122.51 116.35 6.16 1.57e+00 4.06e-01 1.54e+01 ... (remaining 15099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 5513 17.36 - 34.72: 613 34.72 - 52.09: 145 52.09 - 69.45: 33 69.45 - 86.81: 20 Dihedral angle restraints: 6324 sinusoidal: 2492 harmonic: 3832 Sorted by residual: dihedral pdb=" CA ARG C 314 " pdb=" C ARG C 314 " pdb=" N PHE C 315 " pdb=" CA PHE C 315 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ARG B 314 " pdb=" C ARG B 314 " pdb=" N PHE B 315 " pdb=" CA PHE B 315 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ARG D 314 " pdb=" C ARG D 314 " pdb=" N PHE D 315 " pdb=" CA PHE D 315 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 6321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1038 0.039 - 0.079: 465 0.079 - 0.118: 136 0.118 - 0.157: 21 0.157 - 0.197: 4 Chirality restraints: 1664 Sorted by residual: chirality pdb=" CB ILE B 286 " pdb=" CA ILE B 286 " pdb=" CG1 ILE B 286 " pdb=" CG2 ILE B 286 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB ILE A 286 " pdb=" CA ILE A 286 " pdb=" CG1 ILE A 286 " pdb=" CG2 ILE A 286 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CB ILE C 286 " pdb=" CA ILE C 286 " pdb=" CG1 ILE C 286 " pdb=" CG2 ILE C 286 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 1661 not shown) Planarity restraints: 1876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 325 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C THR D 325 " 0.056 2.00e-02 2.50e+03 pdb=" O THR D 325 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 326 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 325 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR A 325 " -0.056 2.00e-02 2.50e+03 pdb=" O THR A 325 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG A 326 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 325 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THR B 325 " -0.056 2.00e-02 2.50e+03 pdb=" O THR B 325 " 0.021 2.00e-02 2.50e+03 pdb=" N ARG B 326 " 0.019 2.00e-02 2.50e+03 ... (remaining 1873 not shown) Histogram of nonbonded interaction distances: 0.05 - 1.07: 7 1.07 - 2.09: 4 2.09 - 3.10: 8077 3.10 - 4.12: 29641 4.12 - 5.14: 64988 Warning: very small nonbonded interaction distances. Nonbonded interactions: 102717 Sorted by model distance: nonbonded pdb=" O HOH B 703 " pdb=" O HOH B 704 " model vdw 0.051 2.440 nonbonded pdb=" O HOH A 702 " pdb=" O HOH A 703 " model vdw 0.057 2.440 nonbonded pdb=" O HOH A 701 " pdb=" O HOH A 702 " model vdw 0.066 2.440 nonbonded pdb=" O HOH B 701 " pdb=" O HOH B 702 " model vdw 0.076 2.440 nonbonded pdb=" O HOH D 702 " pdb=" O HOH D 703 " model vdw 0.079 2.440 ... (remaining 102712 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 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'B' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'C' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) selection = (chain 'D' and (resid 7 through 367 or resid 369 through 448 or resid 450 throug \ h 453 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 72 5.16 5 C 7100 2.51 5 N 1780 2.21 5 O 1842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.460 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 37.230 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 : 0.008 0.093 11100 Z= 0.557 Angle : 0.881 11.354 15104 Z= 0.464 Chirality : 0.047 0.197 1664 Planarity : 0.005 0.046 1876 Dihedral : 16.724 86.809 3852 Min Nonbonded Distance : 0.051 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.91 % Favored : 92.01 % Rotamer Outliers : 5.14 % 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: -3.95 (0.21), residues: 1272 helix: -2.39 (0.15), residues: 772 sheet: None (None), residues: 0 loop : -2.81 (0.29), residues: 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 200 time to evaluate : 1.298 Fit side-chains outliers start: 58 outliers final: 44 residues processed: 254 average time/residue: 0.2854 time to fit residues: 95.3061 Evaluate side-chains 235 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1335 time to fit residues: 10.8772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 60 HIS A 111 GLN A 450 GLN B 19 HIS B 60 HIS B 111 GLN C 19 HIS C 60 HIS C 111 GLN D 19 HIS D 60 HIS D 111 GLN D 409 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11100 Z= 0.225 Angle : 0.584 8.011 15104 Z= 0.302 Chirality : 0.043 0.209 1664 Planarity : 0.006 0.062 1876 Dihedral : 5.679 43.997 1464 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 3.46 % 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: -2.53 (0.23), residues: 1272 helix: -1.14 (0.17), residues: 792 sheet: None (None), residues: 0 loop : -2.47 (0.30), residues: 480 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 193 time to evaluate : 1.294 Fit side-chains outliers start: 39 outliers final: 19 residues processed: 224 average time/residue: 0.2570 time to fit residues: 78.6260 Evaluate side-chains 202 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1441 time to fit residues: 5.8522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.3980 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 450 GLN C 111 GLN C 409 GLN D 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 11100 Z= 0.277 Angle : 0.581 8.916 15104 Z= 0.300 Chirality : 0.044 0.179 1664 Planarity : 0.006 0.065 1876 Dihedral : 5.517 45.106 1464 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 2.39 % 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: -2.16 (0.23), residues: 1272 helix: -0.75 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -2.54 (0.29), residues: 476 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 191 time to evaluate : 1.109 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 211 average time/residue: 0.2558 time to fit residues: 73.4904 Evaluate side-chains 197 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 184 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0983 time to fit residues: 3.9588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.4980 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 111 GLN D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 11100 Z= 0.316 Angle : 0.616 10.312 15104 Z= 0.318 Chirality : 0.045 0.168 1664 Planarity : 0.006 0.070 1876 Dihedral : 5.510 45.248 1464 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer Outliers : 1.86 % 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: -1.97 (0.23), residues: 1272 helix: -0.67 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -2.33 (0.29), residues: 476 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.228 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 204 average time/residue: 0.2734 time to fit residues: 76.5112 Evaluate side-chains 192 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1111 time to fit residues: 3.6651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 112 HIS B 111 GLN B 112 HIS C 111 GLN C 112 HIS D 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 11100 Z= 0.323 Angle : 0.624 10.668 15104 Z= 0.320 Chirality : 0.045 0.167 1664 Planarity : 0.006 0.074 1876 Dihedral : 5.518 45.590 1464 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer Outliers : 1.51 % 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: -1.89 (0.24), residues: 1272 helix: -0.63 (0.18), residues: 796 sheet: None (None), residues: 0 loop : -2.23 (0.29), residues: 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 182 time to evaluate : 1.104 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 196 average time/residue: 0.2793 time to fit residues: 73.9335 Evaluate side-chains 185 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 177 time to evaluate : 1.218 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1036 time to fit residues: 3.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 30 optimal weight: 0.0070 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN C 111 GLN D 111 GLN D 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 11100 Z= 0.194 Angle : 0.568 9.773 15104 Z= 0.289 Chirality : 0.042 0.157 1664 Planarity : 0.006 0.077 1876 Dihedral : 5.197 44.685 1464 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.89 % 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: -1.49 (0.24), residues: 1272 helix: -0.28 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -2.13 (0.28), residues: 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.185 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 191 average time/residue: 0.2718 time to fit residues: 71.0983 Evaluate side-chains 178 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2455 time to fit residues: 3.6290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 90 optimal weight: 0.7980 chunk 104 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 56 optimal weight: 0.0470 chunk 76 optimal weight: 0.9980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 111 GLN D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11100 Z= 0.171 Angle : 0.572 9.540 15104 Z= 0.287 Chirality : 0.041 0.158 1664 Planarity : 0.006 0.079 1876 Dihedral : 5.001 43.456 1464 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.27 % 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: -1.08 (0.24), residues: 1272 helix: 0.02 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -1.85 (0.29), residues: 496 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.285 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 186 average time/residue: 0.2572 time to fit residues: 64.9291 Evaluate side-chains 177 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 43 HIS C 111 GLN C 327 HIS D 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 11100 Z= 0.269 Angle : 0.607 9.051 15104 Z= 0.307 Chirality : 0.044 0.159 1664 Planarity : 0.006 0.080 1876 Dihedral : 5.167 43.945 1464 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.27 % 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: -1.20 (0.24), residues: 1272 helix: -0.21 (0.19), residues: 812 sheet: None (None), residues: 0 loop : -1.75 (0.29), residues: 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.166 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 178 average time/residue: 0.2590 time to fit residues: 62.8786 Evaluate side-chains 174 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0918 time to fit residues: 1.8096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 111 GLN C 327 HIS D 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11100 Z= 0.204 Angle : 0.588 9.109 15104 Z= 0.297 Chirality : 0.042 0.156 1664 Planarity : 0.006 0.079 1876 Dihedral : 5.025 43.372 1464 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer Outliers : 0.27 % 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: -0.96 (0.24), residues: 1272 helix: 0.04 (0.19), residues: 800 sheet: None (None), residues: 0 loop : -1.75 (0.29), residues: 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 1.172 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 175 average time/residue: 0.2792 time to fit residues: 66.1018 Evaluate side-chains 170 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 0.0870 chunk 101 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.0040 chunk 108 optimal weight: 0.8980 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 111 GLN C 327 HIS D 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11100 Z= 0.177 Angle : 0.579 9.123 15104 Z= 0.291 Chirality : 0.042 0.163 1664 Planarity : 0.005 0.080 1876 Dihedral : 4.883 42.351 1464 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.00 % 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: -0.69 (0.24), residues: 1272 helix: 0.28 (0.20), residues: 776 sheet: None (None), residues: 0 loop : -1.60 (0.28), residues: 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.159 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2720 time to fit residues: 63.7681 Evaluate side-chains 173 residues out of total 1116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 101 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN B 111 GLN B 327 HIS C 111 GLN C 327 HIS D 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.098606 restraints weight = 50489.156| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 4.32 r_work: 0.3157 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3810 r_free = 0.3810 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11100 Z= 0.224 Angle : 0.591 8.952 15104 Z= 0.299 Chirality : 0.043 0.171 1664 Planarity : 0.006 0.080 1876 Dihedral : 4.939 42.257 1464 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.09 % 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: -0.68 (0.24), residues: 1272 helix: 0.24 (0.19), residues: 776 sheet: None (None), residues: 0 loop : -1.50 (0.28), residues: 496 =============================================================================== Job complete usr+sys time: 2574.79 seconds wall clock time: 47 minutes 22.98 seconds (2842.98 seconds total)