Starting phenix.real_space_refine on Mon Sep 30 14:40:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/09_2024/8i6m_35200.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/09_2024/8i6m_35200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/09_2024/8i6m_35200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/09_2024/8i6m_35200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/09_2024/8i6m_35200.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6m_35200/09_2024/8i6m_35200.cif" } resolution = 2.59 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= 0.198 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 6 5.21 5 S 108 5.16 5 C 16326 2.51 5 N 4254 2.21 5 O 4764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25464 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} 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: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} 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: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} 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: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} 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: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} 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: 4201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4201 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 504} 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 14.37, per 1000 atoms: 0.56 Number of scatterers: 25464 At special positions: 0 Unit cell: (169.338, 161.226, 98.358, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 6 15.00 Mg 6 11.99 O 4764 8.00 N 4254 7.00 C 16326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.54 Conformation dependent library (CDL) restraints added in 3.3 seconds 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 36 sheets defined 37.5% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.724A 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 98 through 110 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 removed outlier: 3.929A pdb=" N THR A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 269 through 278 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.680A pdb=" N LEU A 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 406 Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 483 through 494 removed outlier: 4.254A pdb=" N PHE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'F' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.724A 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 98 through 110 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 131 Processing helix chain 'F' and resid 146 through 154 removed outlier: 3.582A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 204 removed outlier: 3.928A pdb=" N THR F 202 " --> pdb=" O GLY F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 230 No H-bonds generated for 'chain 'F' and resid 228 through 230' Processing helix chain 'F' and resid 231 through 239 Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 269 through 278 Processing helix chain 'F' and resid 279 through 283 Processing helix chain 'F' and resid 300 through 309 Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.680A pdb=" N LEU F 339 " --> pdb=" O GLN F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 349 Processing helix chain 'F' and resid 395 through 402 Processing helix chain 'F' and resid 403 through 406 Processing helix chain 'F' and resid 440 through 449 Processing helix chain 'F' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE F 494 " --> pdb=" O PHE F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 533 Processing helix chain 'D' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 73 through 87 removed outlier: 3.671A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.724A 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 98 through 110 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 removed outlier: 3.929A pdb=" N THR D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 230 No H-bonds generated for 'chain 'D' and resid 228 through 230' Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 269 through 278 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 300 through 309 Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.680A pdb=" N LEU D 339 " --> pdb=" O GLN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 349 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 403 through 406 Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'C' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.724A 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 98 through 110 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 removed outlier: 3.928A pdb=" N THR C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 269 through 278 Processing helix chain 'C' and resid 279 through 283 Processing helix chain 'C' and resid 300 through 309 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.679A pdb=" N LEU C 339 " --> pdb=" O GLN C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 349 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 403 through 406 Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE C 494 " --> pdb=" O PHE C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 Processing helix chain 'B' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.725A 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 98 through 110 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.928A pdb=" N THR B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 231 through 239 Processing helix chain 'B' and resid 250 through 262 Processing helix chain 'B' and resid 269 through 278 Processing helix chain 'B' and resid 279 through 283 Processing helix chain 'B' and resid 300 through 309 Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.680A pdb=" N LEU B 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 349 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 403 through 406 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE B 494 " --> pdb=" O PHE B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.849A pdb=" N LEU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 73 through 87 removed outlier: 3.670A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.724A 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 98 through 110 Processing helix chain 'E' and resid 120 through 126 Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.581A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 removed outlier: 3.929A pdb=" N THR E 202 " --> pdb=" O GLY E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 230 No H-bonds generated for 'chain 'E' and resid 228 through 230' Processing helix chain 'E' and resid 231 through 239 Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 269 through 278 Processing helix chain 'E' and resid 279 through 283 Processing helix chain 'E' and resid 300 through 309 Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.679A pdb=" N LEU E 339 " --> pdb=" O GLN E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 349 Processing helix chain 'E' and resid 395 through 402 Processing helix chain 'E' and resid 403 through 406 Processing helix chain 'E' and resid 440 through 449 Processing helix chain 'E' and resid 483 through 494 removed outlier: 4.255A pdb=" N PHE E 494 " --> pdb=" O PHE E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.800A pdb=" N GLU A 30 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR A 245 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL A 32 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE A 217 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS A 267 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET A 219 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 266 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.547A pdb=" N ILE A 114 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU A 140 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 116 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 66 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER A 328 " --> pdb=" O TYR A 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 363 removed outlier: 5.502A pdb=" N ASP A 411 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL A 382 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR A 409 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY A 410 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG A 426 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL A 412 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 431 Processing sheet with id=AA6, first strand: chain 'A' and resid 453 through 462 removed outlier: 3.518A pdb=" N GLU A 455 " --> pdb=" O THR A 475 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LYS A 510 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA A 472 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.799A pdb=" N GLU F 30 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR F 245 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL F 32 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE F 217 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N HIS F 267 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET F 219 " --> pdb=" O HIS F 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER F 266 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 136 through 140 removed outlier: 6.548A pdb=" N ILE F 114 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU F 140 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE F 116 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL F 66 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER F 328 " --> pdb=" O TYR F 318 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 361 through 363 removed outlier: 5.502A pdb=" N ASP F 411 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL F 382 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR F 409 " --> pdb=" O VAL F 382 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY F 410 " --> pdb=" O ARG F 426 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG F 426 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL F 412 " --> pdb=" O THR F 424 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 430 through 431 Processing sheet with id=AB3, first strand: chain 'F' and resid 453 through 462 removed outlier: 3.517A pdb=" N GLU F 455 " --> pdb=" O THR F 475 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LYS F 510 " --> pdb=" O PRO F 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA F 472 " --> pdb=" O LYS F 510 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.799A pdb=" N GLU D 30 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR D 245 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL D 32 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE D 217 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS D 267 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET D 219 " --> pdb=" O HIS D 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER D 266 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.547A pdb=" N ILE D 114 " --> pdb=" O VAL D 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU D 140 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE D 116 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL D 66 " --> pdb=" O HIS D 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER D 328 " --> pdb=" O TYR D 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 361 through 363 removed outlier: 5.501A pdb=" N ASP D 411 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N VAL D 382 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR D 409 " --> pdb=" O VAL D 382 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY D 410 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 426 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 412 " --> pdb=" O THR D 424 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 430 through 431 Processing sheet with id=AB9, first strand: chain 'D' and resid 453 through 462 removed outlier: 3.517A pdb=" N GLU D 455 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LYS D 510 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 472 " --> pdb=" O LYS D 510 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.800A pdb=" N GLU C 30 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR C 245 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 32 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE C 217 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS C 267 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET C 219 " --> pdb=" O HIS C 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER C 266 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.547A pdb=" N ILE C 114 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU C 140 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE C 116 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL C 66 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER C 328 " --> pdb=" O TYR C 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 363 removed outlier: 5.502A pdb=" N ASP C 411 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N VAL C 382 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N THR C 409 " --> pdb=" O VAL C 382 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY C 410 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG C 426 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL C 412 " --> pdb=" O THR C 424 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 430 through 431 Processing sheet with id=AC6, first strand: chain 'C' and resid 453 through 462 removed outlier: 3.518A pdb=" N GLU C 455 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N LYS C 510 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA C 472 " --> pdb=" O LYS C 510 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.799A pdb=" N GLU B 30 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR B 245 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 32 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE B 217 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS B 267 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET B 219 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 266 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.547A pdb=" N ILE B 114 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 140 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 116 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER B 328 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 363 removed outlier: 5.502A pdb=" N ASP B 411 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL B 382 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR B 409 " --> pdb=" O VAL B 382 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N GLY B 410 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG B 426 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL B 412 " --> pdb=" O THR B 424 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 430 through 431 Processing sheet with id=AD3, first strand: chain 'B' and resid 453 through 462 removed outlier: 3.518A pdb=" N GLU B 455 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LYS B 510 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 472 " --> pdb=" O LYS B 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.800A pdb=" N GLU E 30 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N TYR E 245 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL E 32 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE E 217 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N HIS E 267 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N MET E 219 " --> pdb=" O HIS E 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER E 266 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 136 through 140 removed outlier: 6.546A pdb=" N ILE E 114 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU E 140 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE E 116 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL E 66 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 317 through 318 removed outlier: 3.800A pdb=" N SER E 328 " --> pdb=" O TYR E 318 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 361 through 363 removed outlier: 5.501A pdb=" N ASP E 411 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N VAL E 382 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR E 409 " --> pdb=" O VAL E 382 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLY E 410 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG E 426 " --> pdb=" O GLY E 410 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL E 412 " --> pdb=" O THR E 424 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 430 through 431 Processing sheet with id=AD9, first strand: chain 'E' and resid 453 through 462 removed outlier: 3.517A pdb=" N GLU E 455 " --> pdb=" O THR E 475 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LYS E 510 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA E 472 " --> pdb=" O LYS E 510 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2430 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: 9.51 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4266 1.28 - 1.41: 6288 1.41 - 1.54: 15155 1.54 - 1.68: 127 1.68 - 1.81: 192 Bond restraints: 26028 Sorted by residual: bond pdb=" CA THR F 202 " pdb=" C THR F 202 " ideal model delta sigma weight residual 1.521 1.413 0.107 9.90e-03 1.02e+04 1.17e+02 bond pdb=" CA THR B 202 " pdb=" C THR B 202 " ideal model delta sigma weight residual 1.521 1.414 0.107 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR E 202 " pdb=" C THR E 202 " ideal model delta sigma weight residual 1.521 1.414 0.107 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR A 202 " pdb=" C THR A 202 " ideal model delta sigma weight residual 1.521 1.414 0.106 9.90e-03 1.02e+04 1.16e+02 bond pdb=" CA THR C 202 " pdb=" C THR C 202 " ideal model delta sigma weight residual 1.521 1.414 0.106 9.90e-03 1.02e+04 1.15e+02 ... (remaining 26023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 34354 2.36 - 4.72: 770 4.72 - 7.08: 108 7.08 - 9.44: 30 9.44 - 11.80: 18 Bond angle restraints: 35280 Sorted by residual: angle pdb=" C THR D 202 " pdb=" CA THR D 202 " pdb=" CB THR D 202 " ideal model delta sigma weight residual 110.08 98.28 11.80 1.57e+00 4.06e-01 5.65e+01 angle pdb=" C THR B 202 " pdb=" CA THR B 202 " pdb=" CB THR B 202 " ideal model delta sigma weight residual 110.08 98.30 11.78 1.57e+00 4.06e-01 5.63e+01 angle pdb=" C THR A 202 " pdb=" CA THR A 202 " pdb=" CB THR A 202 " ideal model delta sigma weight residual 110.08 98.30 11.78 1.57e+00 4.06e-01 5.63e+01 angle pdb=" C THR C 202 " pdb=" CA THR C 202 " pdb=" CB THR C 202 " ideal model delta sigma weight residual 110.08 98.32 11.76 1.57e+00 4.06e-01 5.61e+01 angle pdb=" C THR E 202 " pdb=" CA THR E 202 " pdb=" CB THR E 202 " ideal model delta sigma weight residual 110.08 98.32 11.76 1.57e+00 4.06e-01 5.61e+01 ... (remaining 35275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.81: 14725 26.81 - 53.62: 770 53.62 - 80.43: 78 80.43 - 107.24: 30 107.24 - 134.05: 3 Dihedral angle restraints: 15606 sinusoidal: 6378 harmonic: 9228 Sorted by residual: dihedral pdb=" C5' AMP E1002 " pdb=" O5' AMP E1002 " pdb=" P AMP E1002 " pdb=" O3P AMP E1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.06 -134.05 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' AMP A1002 " pdb=" O5' AMP A1002 " pdb=" P AMP A1002 " pdb=" O3P AMP A1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.05 -134.05 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" C5' AMP C1002 " pdb=" O5' AMP C1002 " pdb=" P AMP C1002 " pdb=" O3P AMP C1002 " ideal model delta sinusoidal sigma weight residual -60.00 74.03 -134.03 1 2.00e+01 2.50e-03 4.07e+01 ... (remaining 15603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3818 0.121 - 0.243: 106 0.243 - 0.364: 42 0.364 - 0.486: 12 0.486 - 0.607: 6 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA MET B 320 " pdb=" N MET B 320 " pdb=" C MET B 320 " pdb=" CB MET B 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA MET F 320 " pdb=" N MET F 320 " pdb=" C MET F 320 " pdb=" CB MET F 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 chirality pdb=" CA MET A 320 " pdb=" N MET A 320 " pdb=" C MET A 320 " pdb=" CB MET A 320 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.20e+00 ... (remaining 3981 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA C1001 " -0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA C1001 " 0.101 2.00e-02 2.50e+03 pdb=" C8 OLA C1001 " -0.101 2.00e-02 2.50e+03 pdb=" C9 OLA C1001 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA D1001 " 0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA D1001 " -0.101 2.00e-02 2.50e+03 pdb=" C8 OLA D1001 " 0.101 2.00e-02 2.50e+03 pdb=" C9 OLA D1001 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLA F1001 " 0.232 2.00e-02 2.50e+03 1.79e-01 3.22e+02 pdb=" C11 OLA F1001 " -0.100 2.00e-02 2.50e+03 pdb=" C8 OLA F1001 " 0.101 2.00e-02 2.50e+03 pdb=" C9 OLA F1001 " -0.233 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 865 2.71 - 3.26: 24714 3.26 - 3.81: 41241 3.81 - 4.35: 55634 4.35 - 4.90: 90516 Nonbonded interactions: 212970 Sorted by model distance: nonbonded pdb=" O1P AMP E1002 " pdb="MG MG E1003 " model vdw 2.165 2.170 nonbonded pdb=" O3P AMP B1002 " pdb="MG MG B1003 " model vdw 2.166 2.170 nonbonded pdb=" O1P AMP C1002 " pdb="MG MG C1003 " model vdw 2.166 2.170 nonbonded pdb=" O1P AMP A1002 " pdb="MG MG A1003 " model vdw 2.166 2.170 nonbonded pdb=" O3P AMP D1002 " pdb="MG MG D1003 " model vdw 2.167 2.170 ... (remaining 212965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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=1.00 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: 2.340 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: 0.850 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 55.570 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 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 : 0.007 0.137 26028 Z= 0.454 Angle : 0.837 11.799 35280 Z= 0.490 Chirality : 0.066 0.607 3984 Planarity : 0.008 0.179 4470 Dihedral : 16.136 134.054 9666 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.17 % Favored : 91.63 % Rotamer: Outliers : 0.80 % Allowed : 18.81 % Favored : 80.39 % Cbeta Deviations : 0.61 % 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: -1.29 (0.15), residues: 3156 helix: 0.06 (0.16), residues: 1074 sheet: -1.22 (0.21), residues: 582 loop : -1.31 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 466 HIS 0.005 0.001 HIS E 228 PHE 0.023 0.002 PHE E 186 TYR 0.013 0.001 TYR E 318 ARG 0.001 0.000 ARG A 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 265 time to evaluate : 3.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.8442 (mtt) cc_final: 0.8103 (mtt) REVERT: D 158 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7951 (mp0) REVERT: D 176 THR cc_start: 0.8097 (t) cc_final: 0.7629 (m) REVERT: D 395 ASN cc_start: 0.8412 (m-40) cc_final: 0.8167 (m110) REVERT: C 58 MET cc_start: 0.8460 (mtt) cc_final: 0.8124 (mtt) REVERT: E 176 THR cc_start: 0.8144 (t) cc_final: 0.7661 (m) REVERT: E 395 ASN cc_start: 0.8389 (m-40) cc_final: 0.8140 (m110) outliers start: 22 outliers final: 4 residues processed: 278 average time/residue: 1.6463 time to fit residues: 521.3437 Evaluate side-chains 214 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 210 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain B residue 163 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 244 optimal weight: 0.0980 chunk 94 optimal weight: 8.9990 chunk 148 optimal weight: 40.0000 chunk 182 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 29 GLN A 117 HIS A 209 GLN A 213 HIS A 226 HIS ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 HIS F 12 GLN F 29 GLN F 117 HIS F 154 GLN F 209 GLN F 213 HIS F 226 HIS F 228 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 408 HIS F 450 HIS D 12 GLN D 29 GLN D 117 HIS D 209 GLN D 213 HIS D 226 HIS D 228 HIS ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 HIS C 6 ASN C 12 GLN C 29 GLN C 117 HIS C 154 GLN C 209 GLN C 213 HIS C 226 HIS C 228 HIS ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 HIS B 6 ASN B 12 GLN B 29 GLN B 117 HIS B 209 GLN B 213 HIS B 226 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS B 450 HIS E 12 GLN E 29 GLN E 117 HIS E 209 GLN E 213 HIS E 226 HIS E 228 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 HIS Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 26028 Z= 0.298 Angle : 0.654 7.201 35280 Z= 0.341 Chirality : 0.049 0.203 3984 Planarity : 0.004 0.041 4470 Dihedral : 8.922 112.165 3560 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.65 % Favored : 91.16 % Rotamer: Outliers : 2.83 % Allowed : 16.34 % Favored : 80.83 % 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: -1.15 (0.15), residues: 3156 helix: 0.53 (0.16), residues: 1080 sheet: -0.97 (0.19), residues: 660 loop : -1.66 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 466 HIS 0.009 0.001 HIS D 228 PHE 0.015 0.002 PHE D 225 TYR 0.013 0.002 TYR A 174 ARG 0.003 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 228 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 42 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8246 (ttpt) REVERT: F 58 MET cc_start: 0.8532 (mtt) cc_final: 0.8184 (mtm) REVERT: F 107 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7336 (t70) REVERT: F 281 LYS cc_start: 0.7466 (ttpp) cc_final: 0.7196 (ttmm) REVERT: D 100 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: D 150 ARG cc_start: 0.7980 (mtm110) cc_final: 0.7594 (mpt-90) REVERT: D 395 ASN cc_start: 0.8333 (m-40) cc_final: 0.8072 (m110) REVERT: C 58 MET cc_start: 0.8529 (mtt) cc_final: 0.8141 (mtt) REVERT: C 107 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7366 (t70) REVERT: C 343 GLN cc_start: 0.7178 (mp10) cc_final: 0.6599 (mt0) REVERT: C 347 TYR cc_start: 0.8487 (m-80) cc_final: 0.8251 (m-80) REVERT: E 100 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: E 150 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7611 (mpt-90) REVERT: E 395 ASN cc_start: 0.8312 (m-40) cc_final: 0.8045 (m110) outliers start: 78 outliers final: 28 residues processed: 290 average time/residue: 1.4454 time to fit residues: 484.0253 Evaluate side-chains 235 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 202 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 61 LYS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 306 optimal weight: 7.9990 chunk 252 optimal weight: 30.0000 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 227 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 26028 Z= 0.337 Angle : 0.660 7.579 35280 Z= 0.344 Chirality : 0.050 0.226 3984 Planarity : 0.005 0.045 4470 Dihedral : 8.854 105.847 3556 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.40 % Favored : 91.41 % Rotamer: Outliers : 3.99 % Allowed : 16.23 % Favored : 79.77 % 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: -1.15 (0.14), residues: 3156 helix: 0.57 (0.16), residues: 1086 sheet: -0.97 (0.19), residues: 660 loop : -1.70 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 402 HIS 0.010 0.002 HIS B 228 PHE 0.016 0.002 PHE D 225 TYR 0.013 0.002 TYR B 174 ARG 0.003 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 213 time to evaluate : 2.602 Fit side-chains REVERT: A 158 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7866 (mm-30) REVERT: F 58 MET cc_start: 0.8592 (mtt) cc_final: 0.8234 (mtm) REVERT: F 107 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7355 (t70) REVERT: F 203 ILE cc_start: 0.8831 (mm) cc_final: 0.8601 (tt) REVERT: F 347 TYR cc_start: 0.8457 (m-80) cc_final: 0.8200 (m-80) REVERT: D 100 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: D 107 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7654 (t70) REVERT: D 150 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7604 (mpt-90) REVERT: D 367 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7511 (mmm) REVERT: D 428 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7450 (mmtp) REVERT: C 58 MET cc_start: 0.8567 (mtt) cc_final: 0.8225 (mtm) REVERT: C 107 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7413 (t70) REVERT: C 260 GLN cc_start: 0.8160 (mm110) cc_final: 0.7593 (tt0) REVERT: C 343 GLN cc_start: 0.7144 (mp10) cc_final: 0.6656 (mt0) REVERT: B 158 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: E 100 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: E 107 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7601 (t70) REVERT: E 150 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7630 (mpt-90) REVERT: E 367 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7535 (mmm) outliers start: 110 outliers final: 30 residues processed: 302 average time/residue: 1.4731 time to fit residues: 512.6993 Evaluate side-chains 239 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 198 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 428 LYS Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 367 MET Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.7980 chunk 213 optimal weight: 0.5980 chunk 147 optimal weight: 10.0000 chunk 31 optimal weight: 0.0970 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 284 optimal weight: 0.7980 chunk 301 optimal weight: 5.9990 chunk 148 optimal weight: 30.0000 chunk 269 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS F 6 ASN ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26028 Z= 0.179 Angle : 0.587 8.634 35280 Z= 0.300 Chirality : 0.046 0.168 3984 Planarity : 0.004 0.039 4470 Dihedral : 8.112 78.233 3556 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.51 % Favored : 92.30 % Rotamer: Outliers : 2.36 % Allowed : 18.12 % Favored : 79.52 % 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: -0.85 (0.15), residues: 3156 helix: 0.88 (0.16), residues: 1080 sheet: -0.84 (0.20), residues: 648 loop : -1.55 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 290 HIS 0.006 0.001 HIS C 267 PHE 0.011 0.001 PHE C 173 TYR 0.008 0.001 TYR C 234 ARG 0.002 0.000 ARG E 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 220 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.8417 (mtt) cc_final: 0.8091 (mtm) REVERT: F 107 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7362 (t70) REVERT: F 347 TYR cc_start: 0.8437 (m-80) cc_final: 0.8206 (m-80) REVERT: D 395 ASN cc_start: 0.8325 (m-40) cc_final: 0.8063 (m110) REVERT: C 58 MET cc_start: 0.8381 (mtt) cc_final: 0.8050 (mtm) REVERT: C 107 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7559 (t70) REVERT: C 343 GLN cc_start: 0.7010 (mp10) cc_final: 0.6592 (mt0) REVERT: E 150 ARG cc_start: 0.7917 (mtm110) cc_final: 0.7601 (mpt-90) REVERT: E 395 ASN cc_start: 0.8303 (m-40) cc_final: 0.8034 (m110) outliers start: 65 outliers final: 27 residues processed: 264 average time/residue: 1.3998 time to fit residues: 427.5324 Evaluate side-chains 227 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 438 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 481 GLN Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 481 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 20.0000 chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 0.0270 chunk 257 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 26028 Z= 0.287 Angle : 0.643 9.401 35280 Z= 0.332 Chirality : 0.048 0.200 3984 Planarity : 0.004 0.041 4470 Dihedral : 8.188 59.391 3556 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.27 % Favored : 91.54 % Rotamer: Outliers : 2.98 % Allowed : 17.72 % Favored : 79.30 % 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: -0.91 (0.15), residues: 3156 helix: 0.83 (0.16), residues: 1086 sheet: -0.87 (0.19), residues: 660 loop : -1.59 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 466 HIS 0.009 0.001 HIS B 228 PHE 0.016 0.002 PHE E 225 TYR 0.011 0.002 TYR A 174 ARG 0.003 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 210 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7874 (mm-30) REVERT: A 505 LEU cc_start: 0.3379 (OUTLIER) cc_final: 0.3138 (mt) REVERT: F 58 MET cc_start: 0.8523 (mtt) cc_final: 0.8138 (mtm) REVERT: F 107 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7318 (t70) REVERT: F 343 GLN cc_start: 0.7061 (mp10) cc_final: 0.6372 (mt0) REVERT: F 347 TYR cc_start: 0.8447 (m-80) cc_final: 0.8202 (m-80) REVERT: D 100 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: D 150 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7582 (mpt-90) REVERT: D 367 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7398 (mmm) REVERT: D 395 ASN cc_start: 0.8415 (m-40) cc_final: 0.8157 (m110) REVERT: C 58 MET cc_start: 0.8489 (mtt) cc_final: 0.8162 (mtm) REVERT: C 107 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7339 (t70) REVERT: C 343 GLN cc_start: 0.7058 (mp10) cc_final: 0.6662 (mt0) REVERT: E 100 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: E 150 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7617 (mpt-90) REVERT: E 395 ASN cc_start: 0.8398 (m-40) cc_final: 0.8146 (m110) REVERT: E 428 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7841 (mmtt) outliers start: 82 outliers final: 40 residues processed: 271 average time/residue: 1.3460 time to fit residues: 424.9253 Evaluate side-chains 251 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 203 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 466 TRP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 481 GLN Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 481 GLN Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 301 optimal weight: 0.2980 chunk 250 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 26028 Z= 0.258 Angle : 0.626 8.162 35280 Z= 0.321 Chirality : 0.048 0.200 3984 Planarity : 0.004 0.041 4470 Dihedral : 8.077 59.444 3556 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.86 % Favored : 91.95 % Rotamer: Outliers : 3.01 % Allowed : 18.37 % Favored : 78.61 % 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: -0.90 (0.15), residues: 3156 helix: 0.84 (0.16), residues: 1086 sheet: -0.87 (0.19), residues: 660 loop : -1.59 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 466 HIS 0.009 0.001 HIS F 267 PHE 0.015 0.002 PHE B 173 TYR 0.009 0.001 TYR C 318 ARG 0.002 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 209 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7873 (mm-30) REVERT: F 58 MET cc_start: 0.8496 (mtt) cc_final: 0.8140 (mtm) REVERT: F 107 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7307 (t70) REVERT: F 203 ILE cc_start: 0.8778 (mm) cc_final: 0.8493 (tt) REVERT: F 343 GLN cc_start: 0.7004 (mp10) cc_final: 0.6473 (mt0) REVERT: F 347 TYR cc_start: 0.8456 (m-80) cc_final: 0.8200 (m-80) REVERT: D 107 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7620 (t70) REVERT: D 150 ARG cc_start: 0.7922 (mtm110) cc_final: 0.7592 (mpt-90) REVERT: D 367 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7355 (mmm) REVERT: D 395 ASN cc_start: 0.8408 (m-40) cc_final: 0.8151 (m110) REVERT: D 505 LEU cc_start: 0.3675 (OUTLIER) cc_final: 0.3290 (mt) REVERT: C 58 MET cc_start: 0.8462 (mtt) cc_final: 0.8096 (mtm) REVERT: C 107 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7339 (t70) REVERT: C 343 GLN cc_start: 0.7052 (mp10) cc_final: 0.6636 (mt0) REVERT: B 418 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: E 107 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7579 (t70) REVERT: E 150 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7619 (mpt-90) REVERT: E 395 ASN cc_start: 0.8431 (m-40) cc_final: 0.8191 (m110) REVERT: E 428 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7868 (mmtt) outliers start: 83 outliers final: 48 residues processed: 269 average time/residue: 1.4109 time to fit residues: 438.3450 Evaluate side-chains 259 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 271 THR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 320 MET Chi-restraints excluded: chain F residue 321 SER Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain F residue 466 TRP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 367 MET Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 321 SER Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain C residue 481 GLN Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 170 optimal weight: 0.6980 chunk 254 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 300 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 183 optimal weight: 0.0970 chunk 138 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS F 154 GLN ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26028 Z= 0.178 Angle : 0.576 6.886 35280 Z= 0.293 Chirality : 0.046 0.167 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.700 61.683 3556 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.46 % Rotamer: Outliers : 1.85 % Allowed : 19.86 % Favored : 78.29 % 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: -0.70 (0.15), residues: 3156 helix: 0.99 (0.16), residues: 1086 sheet: -0.78 (0.20), residues: 648 loop : -1.45 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 466 HIS 0.007 0.001 HIS F 267 PHE 0.011 0.001 PHE B 173 TYR 0.008 0.001 TYR D 234 ARG 0.002 0.000 ARG D 529 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 224 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7169 (pm20) REVERT: A 425 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7155 (t70) REVERT: F 58 MET cc_start: 0.8421 (mtt) cc_final: 0.8063 (mtm) REVERT: F 107 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7354 (t70) REVERT: F 196 THR cc_start: 0.9300 (t) cc_final: 0.9060 (m) REVERT: F 347 TYR cc_start: 0.8434 (m-80) cc_final: 0.8163 (m-80) REVERT: D 150 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7574 (mpt-90) REVERT: D 395 ASN cc_start: 0.8308 (m-40) cc_final: 0.8040 (m110) REVERT: D 505 LEU cc_start: 0.3601 (OUTLIER) cc_final: 0.3219 (mt) REVERT: C 58 MET cc_start: 0.8408 (mtt) cc_final: 0.8061 (mtm) REVERT: C 107 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7586 (t70) REVERT: C 343 GLN cc_start: 0.6979 (mp10) cc_final: 0.6596 (mt0) REVERT: B 274 HIS cc_start: 0.8451 (t-90) cc_final: 0.8188 (t70) REVERT: B 418 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: E 150 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7709 (mpt-90) REVERT: E 395 ASN cc_start: 0.8336 (m-40) cc_final: 0.8073 (m110) outliers start: 51 outliers final: 24 residues processed: 256 average time/residue: 1.4449 time to fit residues: 430.3598 Evaluate side-chains 235 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 204 optimal weight: 10.0000 chunk 148 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26028 Z= 0.249 Angle : 0.622 7.419 35280 Z= 0.319 Chirality : 0.047 0.188 3984 Planarity : 0.004 0.041 4470 Dihedral : 7.895 65.000 3556 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.11 % Favored : 91.70 % Rotamer: Outliers : 1.82 % Allowed : 20.55 % Favored : 77.63 % 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: -0.78 (0.15), residues: 3156 helix: 0.92 (0.16), residues: 1086 sheet: -0.82 (0.20), residues: 660 loop : -1.50 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 466 HIS 0.009 0.001 HIS C 267 PHE 0.013 0.002 PHE E 225 TYR 0.009 0.001 TYR C 318 ARG 0.002 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 214 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 58 MET cc_start: 0.8513 (mtt) cc_final: 0.8236 (mtm) REVERT: F 107 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7286 (t70) REVERT: F 347 TYR cc_start: 0.8454 (m-80) cc_final: 0.8201 (m-80) REVERT: D 150 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7581 (mpt-90) REVERT: D 395 ASN cc_start: 0.8360 (m-40) cc_final: 0.8117 (m110) REVERT: D 505 LEU cc_start: 0.3660 (OUTLIER) cc_final: 0.3213 (mt) REVERT: C 58 MET cc_start: 0.8480 (mtt) cc_final: 0.8206 (mtm) REVERT: C 107 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7319 (t70) REVERT: C 343 GLN cc_start: 0.7075 (mp10) cc_final: 0.6663 (mt0) REVERT: B 274 HIS cc_start: 0.8528 (t-90) cc_final: 0.8270 (t70) REVERT: B 418 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: E 150 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7710 (mpt-90) REVERT: E 395 ASN cc_start: 0.8405 (m-40) cc_final: 0.8156 (m110) REVERT: E 428 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7901 (mmtt) outliers start: 50 outliers final: 32 residues processed: 253 average time/residue: 1.4408 time to fit residues: 421.2446 Evaluate side-chains 248 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 2.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.4980 chunk 288 optimal weight: 3.9990 chunk 262 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 220 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 279 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26028 Z= 0.211 Angle : 0.603 7.161 35280 Z= 0.307 Chirality : 0.046 0.180 3984 Planarity : 0.004 0.040 4470 Dihedral : 7.804 65.260 3556 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 1.67 % Allowed : 20.95 % Favored : 77.38 % 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: -0.74 (0.15), residues: 3156 helix: 0.95 (0.16), residues: 1086 sheet: -0.84 (0.20), residues: 648 loop : -1.44 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 466 HIS 0.007 0.001 HIS F 267 PHE 0.013 0.001 PHE B 173 TYR 0.008 0.001 TYR F 318 ARG 0.002 0.000 ARG D 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 207 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7150 (t70) REVERT: F 58 MET cc_start: 0.8469 (mtt) cc_final: 0.8092 (mtm) REVERT: F 107 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7276 (t70) REVERT: F 347 TYR cc_start: 0.8448 (m-80) cc_final: 0.8211 (m-80) REVERT: D 150 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7574 (mpt-90) REVERT: D 395 ASN cc_start: 0.8339 (m-40) cc_final: 0.8092 (m110) REVERT: D 505 LEU cc_start: 0.3589 (OUTLIER) cc_final: 0.3158 (mt) REVERT: C 58 MET cc_start: 0.8436 (mtt) cc_final: 0.8070 (mtm) REVERT: C 107 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7298 (t70) REVERT: C 343 GLN cc_start: 0.7073 (mp10) cc_final: 0.6679 (mt0) REVERT: B 274 HIS cc_start: 0.8539 (t-90) cc_final: 0.8294 (t70) REVERT: B 320 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.6464 (ttt) REVERT: B 418 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6818 (pm20) REVERT: E 150 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7712 (mpt-90) REVERT: E 395 ASN cc_start: 0.8382 (m-40) cc_final: 0.8118 (m110) REVERT: E 428 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7874 (mmtt) outliers start: 46 outliers final: 29 residues processed: 242 average time/residue: 1.4399 time to fit residues: 402.9539 Evaluate side-chains 241 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 205 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 466 TRP Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 180 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 205 optimal weight: 0.3980 chunk 310 optimal weight: 10.0000 chunk 286 optimal weight: 0.6980 chunk 247 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 ASN ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 26028 Z= 0.188 Angle : 0.590 7.431 35280 Z= 0.300 Chirality : 0.046 0.168 3984 Planarity : 0.004 0.043 4470 Dihedral : 7.569 64.914 3556 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.67 % Favored : 92.14 % Rotamer: Outliers : 1.49 % Allowed : 21.24 % Favored : 77.27 % 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: -0.66 (0.15), residues: 3156 helix: 1.00 (0.16), residues: 1086 sheet: -0.80 (0.20), residues: 648 loop : -1.38 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 466 HIS 0.007 0.001 HIS A 274 PHE 0.012 0.001 PHE B 173 TYR 0.008 0.001 TYR C 234 ARG 0.001 0.000 ARG C 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6312 Ramachandran restraints generated. 3156 Oldfield, 0 Emsley, 3156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 219 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: A 425 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7185 (t70) REVERT: F 58 MET cc_start: 0.8438 (mtt) cc_final: 0.8080 (mtm) REVERT: F 107 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7354 (t70) REVERT: F 347 TYR cc_start: 0.8449 (m-80) cc_final: 0.8177 (m-80) REVERT: D 150 ARG cc_start: 0.7931 (mtm110) cc_final: 0.7665 (mpt-90) REVERT: D 395 ASN cc_start: 0.8332 (m-40) cc_final: 0.8081 (m110) REVERT: D 505 LEU cc_start: 0.3522 (OUTLIER) cc_final: 0.3195 (mt) REVERT: C 58 MET cc_start: 0.8426 (mtt) cc_final: 0.8090 (mtm) REVERT: C 107 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7589 (t70) REVERT: C 343 GLN cc_start: 0.7012 (mp10) cc_final: 0.6595 (mt0) REVERT: C 347 TYR cc_start: 0.8478 (m-80) cc_final: 0.8247 (m-80) REVERT: C 461 MET cc_start: 0.3643 (OUTLIER) cc_final: 0.3182 (tmt) REVERT: B 418 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6820 (pm20) REVERT: E 150 ARG cc_start: 0.7921 (mtm110) cc_final: 0.7705 (mpt-90) REVERT: E 395 ASN cc_start: 0.8366 (m-40) cc_final: 0.8101 (m110) outliers start: 41 outliers final: 29 residues processed: 249 average time/residue: 1.3722 time to fit residues: 395.3231 Evaluate side-chains 244 residues out of total 2778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 208 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 394 ASP Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 466 TRP Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 461 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 228 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 GLN ** B 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** E 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.164680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.105376 restraints weight = 27070.240| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.86 r_work: 0.3087 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26028 Z= 0.212 Angle : 0.607 7.963 35280 Z= 0.310 Chirality : 0.047 0.177 3984 Planarity : 0.004 0.043 4470 Dihedral : 7.609 65.996 3556 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 1.92 % Allowed : 21.06 % Favored : 77.02 % 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: -0.70 (0.15), residues: 3156 helix: 0.98 (0.16), residues: 1086 sheet: -0.82 (0.20), residues: 660 loop : -1.41 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 466 HIS 0.008 0.001 HIS F 267 PHE 0.013 0.001 PHE E 225 TYR 0.008 0.001 TYR C 318 ARG 0.002 0.000 ARG E 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8333.28 seconds wall clock time: 149 minutes 49.82 seconds (8989.82 seconds total)