Starting phenix.real_space_refine on Tue Mar 19 22:20:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i22_35129/03_2024/8i22_35129_neut_updated.pdb" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16296 2.51 5 N 4236 2.21 5 O 4758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 7": "OD1" <-> "OD2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "F ASP 7": "OD1" <-> "OD2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 153": "OE1" <-> "OE2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 346": "OE1" <-> "OE2" Residue "F TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 503": "OE1" <-> "OE2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B ASP 311": "OD1" <-> "OD2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "C ASP 7": "OD1" <-> "OD2" Residue "C ASP 112": "OD1" <-> "OD2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C ASP 311": "OD1" <-> "OD2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 503": "OE1" <-> "OE2" Residue "D ASP 7": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D ASP 311": "OD1" <-> "OD2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 503": "OE1" <-> "OE2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E ASP 112": "OD1" <-> "OD2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 346": "OE1" <-> "OE2" Residue "E TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 503": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25398 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'OBK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.93, per 1000 atoms: 0.51 Number of scatterers: 25398 At special positions: 0 Unit cell: (173.91, 158.1, 92.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4758 8.00 N 4236 7.00 C 16296 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: 9.36 Conformation dependent library (CDL) restraints added in 4.4 seconds 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 114 helices and 42 sheets defined 31.9% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 41 through 57 Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.600A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 118 through 130 Proline residue: A 122 - end of helix removed outlier: 3.520A pdb=" N ASP A 125 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 128 " --> pdb=" O ASP A 125 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLY A 129 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 228 through 239 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 341 through 348 removed outlier: 3.558A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 442 through 447 Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 41 through 57 Processing helix chain 'F' and resid 74 through 85 removed outlier: 3.599A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 118 through 130 Proline residue: F 122 - end of helix removed outlier: 3.520A pdb=" N ASP F 125 " --> pdb=" O PRO F 122 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS F 128 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY F 129 " --> pdb=" O GLN F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 153 Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 228 through 239 Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 270 through 278 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 301 through 309 Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 341 through 348 removed outlier: 3.557A pdb=" N GLU F 346 " --> pdb=" O ASP F 342 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR F 347 " --> pdb=" O GLN F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 442 through 447 Processing helix chain 'F' and resid 484 through 492 Processing helix chain 'F' and resid 525 through 532 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 41 through 57 Processing helix chain 'B' and resid 74 through 85 removed outlier: 3.600A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 130 Proline residue: B 122 - end of helix removed outlier: 3.520A pdb=" N ASP B 125 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS B 128 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLY B 129 " --> pdb=" O GLN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 228 through 239 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 341 through 348 removed outlier: 3.558A pdb=" N GLU B 346 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR B 347 " --> pdb=" O GLN B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 442 through 447 Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 41 through 57 Processing helix chain 'C' and resid 74 through 85 removed outlier: 3.600A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 118 through 130 Proline residue: C 122 - end of helix removed outlier: 3.520A pdb=" N ASP C 125 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS C 128 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLY C 129 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 228 through 239 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 341 through 348 removed outlier: 3.558A pdb=" N GLU C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR C 347 " --> pdb=" O GLN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 442 through 447 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 525 through 532 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 41 through 57 Processing helix chain 'D' and resid 74 through 85 removed outlier: 3.599A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 118 through 130 Proline residue: D 122 - end of helix removed outlier: 3.520A pdb=" N ASP D 125 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 128 " --> pdb=" O ASP D 125 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLY D 129 " --> pdb=" O GLN D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 228 through 239 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 301 through 309 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 341 through 348 removed outlier: 3.559A pdb=" N GLU D 346 " --> pdb=" O ASP D 342 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR D 347 " --> pdb=" O GLN D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 442 through 447 Processing helix chain 'D' and resid 484 through 492 Processing helix chain 'D' and resid 525 through 532 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 41 through 57 Processing helix chain 'E' and resid 74 through 85 removed outlier: 3.600A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 118 through 130 Proline residue: E 122 - end of helix removed outlier: 3.520A pdb=" N ASP E 125 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS E 128 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLY E 129 " --> pdb=" O GLN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 228 through 239 Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 301 through 309 Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 341 through 348 removed outlier: 3.558A pdb=" N GLU E 346 " --> pdb=" O ASP E 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR E 347 " --> pdb=" O GLN E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 442 through 447 Processing helix chain 'E' and resid 484 through 492 Processing helix chain 'E' and resid 525 through 532 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.221A pdb=" N GLN A 243 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 265 " --> pdb=" O MET A 219 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS A 291 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS A 268 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 293 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP A 313 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 294 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE A 315 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.565A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS A 89 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL A 68 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS A 91 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A 172 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 185 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A 174 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS A 183 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 359 through 363 Processing sheet with id= D, first strand: chain 'A' and resid 430 through 433 Processing sheet with id= E, first strand: chain 'A' and resid 457 through 463 Processing sheet with id= F, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= G, first strand: chain 'A' and resid 411 through 415 removed outlier: 3.518A pdb=" N ASP A 425 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.222A pdb=" N GLN F 243 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE F 265 " --> pdb=" O MET F 219 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS F 291 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS F 268 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL F 293 " --> pdb=" O CYS F 268 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP F 313 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE F 294 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE F 315 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.565A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS F 89 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL F 68 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS F 91 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR F 172 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL F 185 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR F 174 " --> pdb=" O LYS F 183 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS F 183 " --> pdb=" O TYR F 174 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 359 through 363 Processing sheet with id= K, first strand: chain 'F' and resid 430 through 433 Processing sheet with id= L, first strand: chain 'F' and resid 457 through 463 Processing sheet with id= M, first strand: chain 'F' and resid 317 through 319 Processing sheet with id= N, first strand: chain 'F' and resid 411 through 415 removed outlier: 3.519A pdb=" N ASP F 425 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.222A pdb=" N GLN B 243 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 265 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS B 291 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS B 268 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL B 293 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP B 313 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE B 294 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE B 315 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 136 through 140 removed outlier: 3.565A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS B 89 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL B 68 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS B 91 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 172 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 185 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR B 174 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LYS B 183 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 359 through 363 Processing sheet with id= R, first strand: chain 'B' and resid 430 through 433 Processing sheet with id= S, first strand: chain 'B' and resid 457 through 463 Processing sheet with id= T, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= U, first strand: chain 'B' and resid 411 through 415 removed outlier: 3.519A pdb=" N ASP B 425 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.222A pdb=" N GLN C 243 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE C 265 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS C 291 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS C 268 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL C 293 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP C 313 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE C 294 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE C 315 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.566A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS C 89 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL C 68 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS C 91 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR C 172 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 185 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR C 174 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS C 183 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 359 through 363 Processing sheet with id= Y, first strand: chain 'C' and resid 430 through 433 Processing sheet with id= Z, first strand: chain 'C' and resid 457 through 463 Processing sheet with id= AA, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= AB, first strand: chain 'C' and resid 411 through 415 removed outlier: 3.517A pdb=" N ASP C 425 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.222A pdb=" N GLN D 243 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE D 265 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS D 291 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS D 268 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL D 293 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP D 313 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE D 294 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE D 315 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.565A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS D 89 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL D 68 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS D 91 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR D 172 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 185 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR D 174 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS D 183 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'D' and resid 359 through 363 Processing sheet with id= AF, first strand: chain 'D' and resid 430 through 433 Processing sheet with id= AG, first strand: chain 'D' and resid 457 through 463 Processing sheet with id= AH, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= AI, first strand: chain 'D' and resid 411 through 415 removed outlier: 3.518A pdb=" N ASP D 425 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.221A pdb=" N GLN E 243 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE E 265 " --> pdb=" O MET E 219 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS E 291 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS E 268 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL E 293 " --> pdb=" O CYS E 268 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP E 313 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE E 294 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N PHE E 315 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.565A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS E 89 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL E 68 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS E 91 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR E 172 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL E 185 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR E 174 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LYS E 183 " --> pdb=" O TYR E 174 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 359 through 363 Processing sheet with id= AM, first strand: chain 'E' and resid 430 through 433 Processing sheet with id= AN, first strand: chain 'E' and resid 457 through 463 Processing sheet with id= AO, first strand: chain 'E' and resid 317 through 319 Processing sheet with id= AP, first strand: chain 'E' and resid 411 through 415 removed outlier: 3.518A pdb=" N ASP E 425 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 1908 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: 8.41 Time building geometry restraints manager: 10.23 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: 4296 1.27 - 1.41: 6253 1.41 - 1.54: 14894 1.54 - 1.67: 327 1.67 - 1.80: 192 Bond restraints: 25962 Sorted by residual: bond pdb=" CA THR F 175 " pdb=" C THR F 175 " ideal model delta sigma weight residual 1.522 1.410 0.112 1.20e-02 6.94e+03 8.66e+01 bond pdb=" CA THR A 175 " pdb=" C THR A 175 " ideal model delta sigma weight residual 1.522 1.411 0.111 1.20e-02 6.94e+03 8.63e+01 bond pdb=" CA THR B 175 " pdb=" C THR B 175 " ideal model delta sigma weight residual 1.522 1.411 0.111 1.20e-02 6.94e+03 8.59e+01 bond pdb=" CA THR D 175 " pdb=" C THR D 175 " ideal model delta sigma weight residual 1.522 1.411 0.111 1.20e-02 6.94e+03 8.56e+01 bond pdb=" CA THR E 175 " pdb=" C THR E 175 " ideal model delta sigma weight residual 1.522 1.411 0.111 1.20e-02 6.94e+03 8.56e+01 ... (remaining 25957 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.68: 514 105.68 - 112.77: 14084 112.77 - 119.86: 8690 119.86 - 126.95: 11580 126.95 - 134.03: 328 Bond angle restraints: 35196 Sorted by residual: angle pdb=" N PRO A 470 " pdb=" CA PRO A 470 " pdb=" C PRO A 470 " ideal model delta sigma weight residual 110.21 120.31 -10.10 1.64e+00 3.72e-01 3.79e+01 angle pdb=" N PRO D 470 " pdb=" CA PRO D 470 " pdb=" C PRO D 470 " ideal model delta sigma weight residual 110.21 120.30 -10.09 1.64e+00 3.72e-01 3.78e+01 angle pdb=" N PRO F 470 " pdb=" CA PRO F 470 " pdb=" C PRO F 470 " ideal model delta sigma weight residual 110.21 120.29 -10.08 1.64e+00 3.72e-01 3.78e+01 angle pdb=" N PRO E 470 " pdb=" CA PRO E 470 " pdb=" C PRO E 470 " ideal model delta sigma weight residual 110.21 120.28 -10.07 1.64e+00 3.72e-01 3.77e+01 angle pdb=" N PRO B 470 " pdb=" CA PRO B 470 " pdb=" C PRO B 470 " ideal model delta sigma weight residual 110.21 120.26 -10.05 1.64e+00 3.72e-01 3.75e+01 ... (remaining 35191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 13417 17.41 - 34.82: 1441 34.82 - 52.23: 505 52.23 - 69.64: 141 69.64 - 87.05: 54 Dihedral angle restraints: 15558 sinusoidal: 6288 harmonic: 9270 Sorted by residual: dihedral pdb=" CA PRO F 325 " pdb=" C PRO F 325 " pdb=" N ILE F 326 " pdb=" CA ILE F 326 " ideal model delta harmonic sigma weight residual -180.00 -157.95 -22.05 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PRO B 325 " pdb=" C PRO B 325 " pdb=" N ILE B 326 " pdb=" CA ILE B 326 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PRO A 325 " pdb=" C PRO A 325 " pdb=" N ILE A 326 " pdb=" CA ILE A 326 " ideal model delta harmonic sigma weight residual -180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 15555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3482 0.082 - 0.164: 428 0.164 - 0.246: 38 0.246 - 0.328: 18 0.328 - 0.409: 12 Chirality restraints: 3978 Sorted by residual: chirality pdb=" CA LYS D 396 " pdb=" N LYS D 396 " pdb=" C LYS D 396 " pdb=" CB LYS D 396 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA LYS F 396 " pdb=" N LYS F 396 " pdb=" C LYS F 396 " pdb=" CB LYS F 396 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA LYS A 396 " pdb=" N LYS A 396 " pdb=" C LYS A 396 " pdb=" CB LYS A 396 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 3975 not shown) Planarity restraints: 4488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 532 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" C HIS B 532 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS B 532 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 533 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 532 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C HIS C 532 " 0.047 2.00e-02 2.50e+03 pdb=" O HIS C 532 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU C 533 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 532 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.35e+00 pdb=" C HIS A 532 " -0.047 2.00e-02 2.50e+03 pdb=" O HIS A 532 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU A 533 " 0.016 2.00e-02 2.50e+03 ... (remaining 4485 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4411 2.77 - 3.30: 24134 3.30 - 3.83: 46938 3.83 - 4.37: 58556 4.37 - 4.90: 92080 Nonbonded interactions: 226119 Sorted by model distance: nonbonded pdb=" OG1 THR B 518 " pdb=" O LYS B 522 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR C 518 " pdb=" O LYS C 522 " model vdw 2.236 2.440 nonbonded pdb=" OG1 THR A 518 " pdb=" O LYS A 522 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR F 518 " pdb=" O LYS F 522 " model vdw 2.237 2.440 nonbonded pdb=" OG1 THR D 518 " pdb=" O LYS D 522 " model vdw 2.237 2.440 ... (remaining 226114 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 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: 1.990 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: 0.020 Extract box with map and model: 9.090 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 65.890 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.160 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.006 0.129 25962 Z= 0.413 Angle : 0.691 10.703 35196 Z= 0.413 Chirality : 0.058 0.409 3978 Planarity : 0.005 0.051 4488 Dihedral : 17.819 87.050 9594 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.88 % Favored : 95.93 % Rotamer: Outliers : 0.65 % Allowed : 17.35 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.28 (0.14), residues: 3168 helix: 0.73 (0.16), residues: 1080 sheet: 0.14 (0.22), residues: 522 loop : -0.92 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 290 HIS 0.011 0.001 HIS C 45 PHE 0.011 0.001 PHE B 225 TYR 0.011 0.001 TYR E 245 ARG 0.004 0.000 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 308 time to evaluate : 3.011 Fit side-chains REVERT: F 197 MET cc_start: 0.8637 (mmp) cc_final: 0.8126 (mtp) REVERT: C 197 MET cc_start: 0.8636 (mmp) cc_final: 0.8124 (mtp) outliers start: 18 outliers final: 9 residues processed: 326 average time/residue: 1.5540 time to fit residues: 575.6947 Evaluate side-chains 261 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 252 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 185 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN D 260 GLN E 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 25962 Z= 0.265 Angle : 0.572 7.524 35196 Z= 0.303 Chirality : 0.047 0.142 3978 Planarity : 0.004 0.041 4488 Dihedral : 6.653 72.168 3474 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.66 % Favored : 95.96 % Rotamer: Outliers : 2.42 % Allowed : 15.00 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.17 (0.14), residues: 3168 helix: 0.74 (0.16), residues: 1068 sheet: 0.12 (0.21), residues: 510 loop : -0.73 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 402 HIS 0.004 0.001 HIS F 195 PHE 0.017 0.002 PHE A 187 TYR 0.017 0.002 TYR B 245 ARG 0.003 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 269 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 430 MET cc_start: 0.7864 (tpt) cc_final: 0.7619 (tpt) REVERT: F 197 MET cc_start: 0.8609 (mmp) cc_final: 0.8155 (mtp) REVERT: F 309 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: B 113 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8366 (mt) REVERT: B 430 MET cc_start: 0.7874 (tpt) cc_final: 0.7639 (tpt) REVERT: C 197 MET cc_start: 0.8609 (mmp) cc_final: 0.8154 (mtp) REVERT: C 309 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: D 288 SER cc_start: 0.8235 (m) cc_final: 0.8030 (p) REVERT: E 288 SER cc_start: 0.8229 (m) cc_final: 0.8027 (p) outliers start: 67 outliers final: 13 residues processed: 330 average time/residue: 1.4288 time to fit residues: 542.3844 Evaluate side-chains 272 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain E residue 436 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 312 optimal weight: 0.0270 chunk 257 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 30.0000 chunk 232 optimal weight: 2.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 260 GLN F 390 ASN C 260 GLN C 390 ASN D 154 GLN D 260 GLN D 395 ASN E 154 GLN E 260 GLN E 395 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25962 Z= 0.358 Angle : 0.612 7.940 35196 Z= 0.326 Chirality : 0.050 0.145 3978 Planarity : 0.005 0.037 4488 Dihedral : 6.768 73.620 3466 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.23 % Favored : 95.52 % Rotamer: Outliers : 2.42 % Allowed : 14.71 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.18 (0.14), residues: 3168 helix: 0.57 (0.16), residues: 1068 sheet: 0.10 (0.21), residues: 510 loop : -0.60 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 402 HIS 0.007 0.001 HIS C 213 PHE 0.019 0.002 PHE C 187 TYR 0.020 0.002 TYR A 245 ARG 0.004 0.001 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 265 time to evaluate : 3.027 Fit side-chains REVERT: A 197 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8107 (mpm) REVERT: A 430 MET cc_start: 0.7886 (tpt) cc_final: 0.7628 (tpt) REVERT: F 140 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8378 (mt) REVERT: F 232 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8761 (mm) REVERT: F 309 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: B 430 MET cc_start: 0.7876 (tpt) cc_final: 0.7614 (tpt) REVERT: C 140 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8366 (mt) REVERT: C 232 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8760 (mm) REVERT: C 309 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7791 (mt-10) outliers start: 67 outliers final: 23 residues processed: 324 average time/residue: 1.5117 time to fit residues: 559.4014 Evaluate side-chains 290 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 260 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain E residue 221 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 306 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 20.0000 chunk 32 optimal weight: 0.6980 chunk 138 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 290 optimal weight: 0.9980 chunk 307 optimal weight: 0.0000 chunk 151 optimal weight: 30.0000 chunk 275 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 154 GLN C 154 GLN D 154 GLN D 260 GLN E 154 GLN E 260 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25962 Z= 0.149 Angle : 0.502 7.311 35196 Z= 0.267 Chirality : 0.044 0.139 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.468 76.711 3465 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.54 % Favored : 96.09 % Rotamer: Outliers : 1.77 % Allowed : 16.02 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.06 (0.15), residues: 3168 helix: 0.77 (0.16), residues: 1068 sheet: 0.05 (0.21), residues: 510 loop : -0.57 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 437 HIS 0.003 0.001 HIS D 39 PHE 0.013 0.001 PHE B 225 TYR 0.012 0.001 TYR B 245 ARG 0.002 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 3.024 Fit side-chains REVERT: A 197 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8207 (mpm) REVERT: F 197 MET cc_start: 0.8665 (mmp) cc_final: 0.8132 (mtp) REVERT: B 197 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8114 (mpm) REVERT: C 197 MET cc_start: 0.8666 (mmp) cc_final: 0.8131 (mtp) REVERT: D 113 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8321 (mt) REVERT: D 232 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8427 (mm) REVERT: E 113 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8302 (mt) REVERT: E 232 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8424 (mm) REVERT: E 428 LYS cc_start: 0.8441 (mttm) cc_final: 0.8230 (mmtm) outliers start: 49 outliers final: 16 residues processed: 310 average time/residue: 1.4165 time to fit residues: 504.8949 Evaluate side-chains 282 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 260 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 306 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.3980 chunk 174 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 262 optimal weight: 9.9990 chunk 212 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 156 optimal weight: 30.0000 chunk 275 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 260 GLN E 154 GLN E 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25962 Z= 0.308 Angle : 0.574 7.757 35196 Z= 0.306 Chirality : 0.048 0.144 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.639 74.777 3462 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.98 % Favored : 95.64 % Rotamer: Outliers : 1.55 % Allowed : 16.59 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.11 (0.15), residues: 3168 helix: 0.64 (0.16), residues: 1068 sheet: -0.02 (0.21), residues: 510 loop : -0.51 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 402 HIS 0.004 0.001 HIS F 213 PHE 0.018 0.002 PHE A 187 TYR 0.018 0.002 TYR A 245 ARG 0.003 0.001 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 260 time to evaluate : 3.150 Fit side-chains REVERT: F 197 MET cc_start: 0.8703 (mmp) cc_final: 0.8194 (mtp) REVERT: F 309 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: F 343 GLN cc_start: 0.8602 (mt0) cc_final: 0.8379 (mt0) REVERT: C 197 MET cc_start: 0.8704 (mmp) cc_final: 0.8194 (mtp) REVERT: C 309 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: C 343 GLN cc_start: 0.8600 (mt0) cc_final: 0.8377 (mt0) REVERT: D 232 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8438 (mm) REVERT: E 232 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8438 (mm) outliers start: 43 outliers final: 22 residues processed: 297 average time/residue: 1.4153 time to fit residues: 483.0794 Evaluate side-chains 278 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 252 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 306 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.0770 chunk 276 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 5.9990 chunk 255 optimal weight: 0.0370 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 161 optimal weight: 0.0060 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN E 154 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25962 Z= 0.125 Angle : 0.477 6.994 35196 Z= 0.254 Chirality : 0.043 0.137 3978 Planarity : 0.003 0.031 4488 Dihedral : 6.282 77.195 3462 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.79 % Favored : 95.83 % Rotamer: Outliers : 1.45 % Allowed : 16.92 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.06 (0.15), residues: 3168 helix: 0.86 (0.16), residues: 1074 sheet: 0.08 (0.21), residues: 510 loop : -0.48 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 437 HIS 0.003 0.001 HIS F 39 PHE 0.011 0.001 PHE B 225 TYR 0.010 0.001 TYR B 245 ARG 0.002 0.000 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 2.761 Fit side-chains REVERT: A 197 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8117 (mpm) REVERT: A 256 ASN cc_start: 0.8517 (t0) cc_final: 0.8313 (t0) REVERT: A 430 MET cc_start: 0.7365 (tpt) cc_final: 0.7147 (tpt) REVERT: F 197 MET cc_start: 0.8540 (mmp) cc_final: 0.8080 (mtp) REVERT: F 309 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: B 197 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8078 (mpm) REVERT: B 430 MET cc_start: 0.7364 (tpt) cc_final: 0.7149 (tpt) REVERT: C 197 MET cc_start: 0.8541 (mmp) cc_final: 0.8082 (mtp) REVERT: C 309 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7747 (mt-10) REVERT: D 113 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8133 (mt) REVERT: D 232 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8381 (mm) REVERT: D 281 LYS cc_start: 0.8549 (ttpt) cc_final: 0.7853 (ttpt) REVERT: E 113 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8136 (mt) REVERT: E 232 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8379 (mm) REVERT: E 281 LYS cc_start: 0.8545 (ttpt) cc_final: 0.7850 (ttpt) REVERT: E 428 LYS cc_start: 0.8456 (mttm) cc_final: 0.8230 (mmtm) outliers start: 40 outliers final: 15 residues processed: 311 average time/residue: 1.3947 time to fit residues: 502.0727 Evaluate side-chains 288 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 265 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 285 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 174 optimal weight: 3.9990 chunk 259 optimal weight: 8.9990 chunk 171 optimal weight: 0.2980 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 154 GLN C 154 GLN D 154 GLN E 154 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25962 Z= 0.220 Angle : 0.527 7.380 35196 Z= 0.279 Chirality : 0.046 0.139 3978 Planarity : 0.004 0.031 4488 Dihedral : 6.407 76.761 3462 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.88 % Favored : 95.74 % Rotamer: Outliers : 1.37 % Allowed : 17.03 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.03 (0.15), residues: 3168 helix: 0.80 (0.16), residues: 1074 sheet: 0.04 (0.21), residues: 510 loop : -0.46 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 402 HIS 0.003 0.001 HIS E 39 PHE 0.014 0.002 PHE B 225 TYR 0.016 0.001 TYR B 245 ARG 0.004 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 258 time to evaluate : 2.955 Fit side-chains REVERT: F 197 MET cc_start: 0.8527 (mmp) cc_final: 0.8121 (mtp) REVERT: F 309 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7796 (mt-10) REVERT: C 197 MET cc_start: 0.8534 (mmp) cc_final: 0.8120 (mtp) REVERT: C 309 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: D 113 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8389 (mt) REVERT: D 232 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8401 (mm) REVERT: E 113 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8379 (mt) REVERT: E 232 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8402 (mm) outliers start: 38 outliers final: 19 residues processed: 291 average time/residue: 1.4206 time to fit residues: 475.3505 Evaluate side-chains 279 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 254 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 183 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 0.4980 chunk 208 optimal weight: 4.9990 chunk 151 optimal weight: 0.0010 chunk 28 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 154 GLN B 331 GLN C 154 GLN C 331 GLN C 343 GLN D 154 GLN E 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25962 Z= 0.135 Angle : 0.479 6.984 35196 Z= 0.253 Chirality : 0.044 0.137 3978 Planarity : 0.003 0.030 4488 Dihedral : 6.220 78.539 3462 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.85 % Favored : 95.77 % Rotamer: Outliers : 1.12 % Allowed : 17.35 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.12 (0.15), residues: 3168 helix: 0.93 (0.16), residues: 1074 sheet: 0.08 (0.21), residues: 510 loop : -0.45 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 437 HIS 0.003 0.001 HIS E 39 PHE 0.012 0.001 PHE B 225 TYR 0.010 0.001 TYR E 245 ARG 0.002 0.000 ARG F 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 264 time to evaluate : 2.736 Fit side-chains REVERT: A 197 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8036 (mpm) REVERT: F 197 MET cc_start: 0.8390 (mmp) cc_final: 0.8089 (mtp) REVERT: F 232 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8664 (mm) REVERT: F 309 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: B 197 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7993 (mpm) REVERT: C 197 MET cc_start: 0.8385 (mmp) cc_final: 0.8094 (mtp) REVERT: C 309 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: D 113 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7999 (mt) REVERT: D 232 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8382 (mm) REVERT: D 281 LYS cc_start: 0.8500 (ttpt) cc_final: 0.7737 (ttpt) REVERT: E 113 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8005 (mt) REVERT: E 232 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8381 (mm) REVERT: E 428 LYS cc_start: 0.8445 (mttm) cc_final: 0.8211 (mmtm) outliers start: 31 outliers final: 14 residues processed: 291 average time/residue: 1.4275 time to fit residues: 477.6206 Evaluate side-chains 279 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 2.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.5980 chunk 293 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 154 GLN B 154 GLN C 154 GLN C 343 GLN D 154 GLN E 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25962 Z= 0.229 Angle : 0.534 8.219 35196 Z= 0.282 Chirality : 0.046 0.146 3978 Planarity : 0.004 0.030 4488 Dihedral : 6.399 77.841 3462 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.50 % Favored : 96.12 % Rotamer: Outliers : 1.19 % Allowed : 17.50 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.05 (0.15), residues: 3168 helix: 0.81 (0.16), residues: 1074 sheet: 0.05 (0.21), residues: 510 loop : -0.43 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 402 HIS 0.004 0.001 HIS C 213 PHE 0.015 0.002 PHE B 225 TYR 0.015 0.001 TYR B 245 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 263 time to evaluate : 3.128 Fit side-chains REVERT: F 197 MET cc_start: 0.8588 (mmp) cc_final: 0.8239 (mtp) REVERT: F 309 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: C 197 MET cc_start: 0.8564 (mmp) cc_final: 0.8266 (mtp) REVERT: C 309 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: D 113 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8412 (mt) REVERT: D 232 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8404 (mm) REVERT: E 113 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8397 (mt) REVERT: E 232 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8405 (mm) outliers start: 33 outliers final: 18 residues processed: 291 average time/residue: 1.4330 time to fit residues: 479.5070 Evaluate side-chains 281 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 4.9990 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 0.3980 chunk 143 optimal weight: 7.9990 chunk 209 optimal weight: 10.0000 chunk 316 optimal weight: 0.0010 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 overall best weight: 2.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 154 GLN B 154 GLN C 154 GLN D 154 GLN E 154 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25962 Z= 0.347 Angle : 0.604 10.383 35196 Z= 0.319 Chirality : 0.050 0.168 3978 Planarity : 0.004 0.032 4488 Dihedral : 6.617 74.246 3462 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.54 % Favored : 96.09 % Rotamer: Outliers : 0.94 % Allowed : 17.61 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.04 (0.15), residues: 3168 helix: 0.68 (0.16), residues: 1062 sheet: -0.04 (0.21), residues: 510 loop : -0.42 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 402 HIS 0.005 0.001 HIS E 39 PHE 0.017 0.002 PHE B 187 TYR 0.020 0.002 TYR A 245 ARG 0.004 0.001 ARG B 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6336 Ramachandran restraints generated. 3168 Oldfield, 0 Emsley, 3168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 267 time to evaluate : 2.863 Fit side-chains REVERT: F 309 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: C 309 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: C 344 GLN cc_start: 0.8544 (pt0) cc_final: 0.8325 (pt0) REVERT: D 232 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8456 (mm) REVERT: E 232 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8457 (mm) outliers start: 26 outliers final: 17 residues processed: 290 average time/residue: 1.4206 time to fit residues: 474.2293 Evaluate side-chains 280 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 259 time to evaluate : 2.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain F residue 221 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 306 SER Chi-restraints excluded: chain F residue 309 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 306 SER Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 252 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 259 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN F 154 GLN F 344 GLN B 154 GLN C 154 GLN D 154 GLN D 260 GLN E 154 GLN E 260 GLN E 331 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.165446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097328 restraints weight = 23710.571| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.01 r_work: 0.3059 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25962 Z= 0.252 Angle : 0.551 9.996 35196 Z= 0.292 Chirality : 0.047 0.157 3978 Planarity : 0.004 0.031 4488 Dihedral : 6.475 73.653 3462 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.50 % Favored : 96.12 % Rotamer: Outliers : 1.05 % Allowed : 17.43 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.00 (0.15), residues: 3168 helix: 0.73 (0.16), residues: 1068 sheet: -0.08 (0.21), residues: 510 loop : -0.38 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 402 HIS 0.004 0.001 HIS D 39 PHE 0.016 0.002 PHE A 187 TYR 0.017 0.002 TYR A 245 ARG 0.004 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9409.75 seconds wall clock time: 167 minutes 45.84 seconds (10065.84 seconds total)