Starting phenix.real_space_refine on Sat Mar 16 05:49:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/03_2024/8op9_17045_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/03_2024/8op9_17045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/03_2024/8op9_17045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/03_2024/8op9_17045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/03_2024/8op9_17045_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/03_2024/8op9_17045_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 Cl 1 4.86 5 C 9070 2.51 5 N 2195 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13811 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {' CL': 1, 'ABU': 2, 'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ABU': 2, 'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Unusual residues: {'ABU': 1, 'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.94, per 1000 atoms: 0.50 Number of scatterers: 13811 At special positions: 0 Unit cell: (95.0235, 97.6815, 137.551, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 75 16.00 O 2470 8.00 N 2195 7.00 C 9070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 602 " - " ASN A 140 " " NAG A 603 " - " ASN A 234 " " NAG B 501 " - " ASN B 140 " " NAG B 502 " - " ASN B 234 " " NAG C 603 " - " ASN C 140 " " NAG C 604 " - " ASN C 234 " " NAG D 501 " - " ASN D 140 " " NAG D 502 " - " ASN D 234 " " NAG E 602 " - " ASN E 140 " " NAG E 603 " - " ASN E 234 " Time building additional restraints: 4.99 Conformation dependent library (CDL) restraints added in 2.1 seconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 30 sheets defined 36.7% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.601A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 282 through 299 removed outlier: 5.008A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.533A pdb=" N SER A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 310 through 334 Proline residue: A 315 - end of helix removed outlier: 4.210A pdb=" N SER A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 379 removed outlier: 3.608A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 477 removed outlier: 4.072A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.601A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 282 through 299 removed outlier: 5.007A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.532A pdb=" N SER B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 310 through 334 Proline residue: B 315 - end of helix removed outlier: 4.210A pdb=" N SER B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 379 removed outlier: 3.609A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 477 removed outlier: 4.072A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.600A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 282 through 299 removed outlier: 5.009A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.534A pdb=" N SER C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 310 through 334 Proline residue: C 315 - end of helix removed outlier: 4.210A pdb=" N SER C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 379 removed outlier: 3.608A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 477 removed outlier: 4.072A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.600A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 282 through 299 removed outlier: 5.009A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.533A pdb=" N SER D 299 " --> pdb=" O MET D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 310 through 334 Proline residue: D 315 - end of helix removed outlier: 4.210A pdb=" N SER D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 379 removed outlier: 3.608A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 477 removed outlier: 4.072A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.601A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 282 through 299 removed outlier: 5.009A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.533A pdb=" N SER E 299 " --> pdb=" O MET E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 303 No H-bonds generated for 'chain 'E' and resid 301 through 303' Processing helix chain 'E' and resid 310 through 334 Proline residue: E 315 - end of helix removed outlier: 4.210A pdb=" N SER E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 379 removed outlier: 3.609A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 477 removed outlier: 4.073A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.386A pdb=" N ILE A 97 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR A 229 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 99 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU A 178 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.818A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.710A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 254 through 262 Processing sheet with id= F, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.027A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 226 through 230 removed outlier: 6.386A pdb=" N ILE B 97 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR B 229 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 99 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B 178 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= I, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.818A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.709A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 254 through 262 Processing sheet with id= L, first strand: chain 'B' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 226 through 230 removed outlier: 6.386A pdb=" N ILE C 97 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR C 229 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 99 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU C 178 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= O, first strand: chain 'C' and resid 110 through 112 removed outlier: 3.818A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.710A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 254 through 262 Processing sheet with id= R, first strand: chain 'C' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.386A pdb=" N ILE D 97 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR D 229 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL D 99 " --> pdb=" O TYR D 229 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 178 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 103 through 105 Processing sheet with id= U, first strand: chain 'D' and resid 110 through 112 removed outlier: 3.818A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.708A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 254 through 262 Processing sheet with id= X, first strand: chain 'D' and resid 163 through 168 removed outlier: 7.027A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 226 through 230 removed outlier: 6.386A pdb=" N ILE E 97 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR E 229 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL E 99 " --> pdb=" O TYR E 229 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU E 178 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 103 through 105 Processing sheet with id= AA, first strand: chain 'E' and resid 110 through 112 removed outlier: 3.818A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.709A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 254 through 262 Processing sheet with id= AD, first strand: chain 'E' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) 665 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.95 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4105 1.34 - 1.46: 3298 1.46 - 1.58: 6607 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14150 Sorted by residual: bond pdb=" C2 HEX C 608 " pdb=" C3 HEX C 608 " ideal model delta sigma weight residual 1.524 1.554 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C4 HEX E 607 " pdb=" C5 HEX E 607 " ideal model delta sigma weight residual 1.524 1.554 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C2 HEX E 607 " pdb=" C3 HEX E 607 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C2 HEX D 506 " pdb=" C3 HEX D 506 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C4 HEX C 608 " pdb=" C5 HEX C 608 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 14145 not shown) Histogram of bond angle deviations from ideal: 100.45 - 107.17: 414 107.17 - 113.88: 8084 113.88 - 120.59: 5397 120.59 - 127.30: 5132 127.30 - 134.01: 168 Bond angle restraints: 19195 Sorted by residual: angle pdb=" CA TYR E 362 " pdb=" CB TYR E 362 " pdb=" CG TYR E 362 " ideal model delta sigma weight residual 113.90 109.23 4.67 1.80e+00 3.09e-01 6.73e+00 angle pdb=" CA TYR B 362 " pdb=" CB TYR B 362 " pdb=" CG TYR B 362 " ideal model delta sigma weight residual 113.90 109.24 4.66 1.80e+00 3.09e-01 6.69e+00 angle pdb=" CA TYR A 362 " pdb=" CB TYR A 362 " pdb=" CG TYR A 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.69e+00 angle pdb=" CA TYR C 362 " pdb=" CB TYR C 362 " pdb=" CG TYR C 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.68e+00 angle pdb=" CA TYR D 362 " pdb=" CB TYR D 362 " pdb=" CG TYR D 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.66e+00 ... (remaining 19190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 8130 16.19 - 32.38: 215 32.38 - 48.57: 35 48.57 - 64.77: 5 64.77 - 80.96: 10 Dihedral angle restraints: 8395 sinusoidal: 3440 harmonic: 4955 Sorted by residual: dihedral pdb=" CA SER D 107 " pdb=" C SER D 107 " pdb=" N LEU D 108 " pdb=" CA LEU D 108 " ideal model delta harmonic sigma weight residual 180.00 164.27 15.73 0 5.00e+00 4.00e-02 9.90e+00 dihedral pdb=" CA SER A 107 " pdb=" C SER A 107 " pdb=" N LEU A 108 " pdb=" CA LEU A 108 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 dihedral pdb=" CA SER B 107 " pdb=" C SER B 107 " pdb=" N LEU B 108 " pdb=" CA LEU B 108 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 ... (remaining 8392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1648 0.044 - 0.088: 411 0.088 - 0.132: 136 0.132 - 0.176: 10 0.176 - 0.219: 5 Chirality restraints: 2210 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 140 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 140 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2207 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.276 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" CG ASN D 234 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG D 502 " 0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.276 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" CG ASN A 234 " 0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.486 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.276 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" CG ASN B 234 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.397 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 65 2.59 - 3.17: 10759 3.17 - 3.74: 20347 3.74 - 4.32: 29697 4.32 - 4.90: 49456 Nonbonded interactions: 110324 Sorted by model distance: nonbonded pdb=" OD1 ASN C 234 " pdb=" O5 NAG C 604 " model vdw 2.012 3.040 nonbonded pdb=" OD1 ASN D 234 " pdb=" O5 NAG D 502 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN A 234 " pdb=" O5 NAG A 603 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN B 234 " pdb=" O5 NAG B 502 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN E 234 " pdb=" O5 NAG E 603 " model vdw 2.014 3.040 ... (remaining 110319 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 78 through 479 or resid 605 through 606)) selection = (chain 'B' and (resid 78 through 479 or resid 505 through 506)) selection = (chain 'C' and (resid 78 through 479 or resid 605 through 606)) selection = (chain 'D' and (resid 78 through 479 or resid 505 through 506)) selection = (chain 'E' and (resid 78 through 479 or resid 605 through 606)) } 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.210 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 39.110 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14150 Z= 0.168 Angle : 0.546 5.097 19195 Z= 0.285 Chirality : 0.043 0.219 2210 Planarity : 0.004 0.029 2330 Dihedral : 8.964 80.958 5160 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.21), residues: 1640 helix: 1.73 (0.21), residues: 600 sheet: 1.63 (0.24), residues: 395 loop : 0.94 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 475 HIS 0.002 0.000 HIS E 84 PHE 0.010 0.001 PHE D 253 TYR 0.019 0.001 TYR D 362 ARG 0.003 0.001 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 331 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.8107 (m) cc_final: 0.7869 (p) REVERT: C 143 MET cc_start: 0.7993 (mmm) cc_final: 0.7782 (mmt) REVERT: D 326 THR cc_start: 0.7879 (m) cc_final: 0.7652 (p) REVERT: D 349 TRP cc_start: 0.6951 (m100) cc_final: 0.6481 (m100) REVERT: E 335 MET cc_start: 0.4174 (mmm) cc_final: 0.3965 (mpp) outliers start: 5 outliers final: 0 residues processed: 336 average time/residue: 0.2778 time to fit residues: 131.7097 Evaluate side-chains 215 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.0870 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN C 287 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 14150 Z= 0.548 Angle : 0.803 8.821 19195 Z= 0.431 Chirality : 0.056 0.428 2210 Planarity : 0.006 0.047 2330 Dihedral : 8.241 89.241 2115 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.50 % Allowed : 6.60 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.57 (0.19), residues: 1640 helix: 0.70 (0.20), residues: 595 sheet: 0.85 (0.24), residues: 400 loop : -0.09 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 128 HIS 0.010 0.002 HIS B 280 PHE 0.027 0.003 PHE D 159 TYR 0.027 0.003 TYR E 188 ARG 0.007 0.001 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 253 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7836 (ptp90) cc_final: 0.7576 (ptp90) REVERT: B 319 THR cc_start: 0.8230 (m) cc_final: 0.7910 (p) REVERT: C 115 ASP cc_start: 0.8183 (m-30) cc_final: 0.7886 (m-30) REVERT: C 158 MET cc_start: 0.7956 (mmm) cc_final: 0.7725 (mmm) REVERT: C 170 ASP cc_start: 0.8068 (p0) cc_final: 0.7837 (p0) REVERT: C 215 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8101 (mt-10) REVERT: C 298 LEU cc_start: 0.8226 (tp) cc_final: 0.7997 (tt) REVERT: D 170 ASP cc_start: 0.8002 (p0) cc_final: 0.7581 (p0) REVERT: D 203 SER cc_start: 0.8607 (t) cc_final: 0.7844 (p) REVERT: D 225 ASP cc_start: 0.8168 (m-30) cc_final: 0.7944 (m-30) REVERT: D 235 ASP cc_start: 0.7140 (m-30) cc_final: 0.6920 (t0) REVERT: D 298 LEU cc_start: 0.8059 (mt) cc_final: 0.7828 (tt) REVERT: E 298 LEU cc_start: 0.7970 (mt) cc_final: 0.7552 (tt) outliers start: 52 outliers final: 40 residues processed: 292 average time/residue: 0.2945 time to fit residues: 119.4450 Evaluate side-chains 253 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 213 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 TYR Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14150 Z= 0.272 Angle : 0.560 5.503 19195 Z= 0.303 Chirality : 0.048 0.404 2210 Planarity : 0.004 0.043 2330 Dihedral : 7.133 89.626 2115 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.97 % Allowed : 8.75 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 0.97 (0.20), residues: 1640 helix: 1.25 (0.21), residues: 600 sheet: 0.88 (0.25), residues: 420 loop : -0.00 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 230 HIS 0.004 0.001 HIS E 254 PHE 0.015 0.002 PHE A 282 TYR 0.022 0.002 TYR E 362 ARG 0.005 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 219 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7758 (ptp90) cc_final: 0.7384 (ptp90) REVERT: C 115 ASP cc_start: 0.7920 (m-30) cc_final: 0.7647 (m-30) REVERT: C 158 MET cc_start: 0.7995 (mmm) cc_final: 0.7747 (mmm) REVERT: C 170 ASP cc_start: 0.8157 (p0) cc_final: 0.7732 (p0) REVERT: C 298 LEU cc_start: 0.8159 (tp) cc_final: 0.7958 (tt) REVERT: C 457 LYS cc_start: 0.7911 (tttt) cc_final: 0.7400 (ttpp) REVERT: D 158 MET cc_start: 0.7946 (mmm) cc_final: 0.7742 (mmm) REVERT: D 170 ASP cc_start: 0.8091 (p0) cc_final: 0.7660 (p0) REVERT: D 185 LYS cc_start: 0.8259 (mttp) cc_final: 0.8027 (mtpp) REVERT: D 197 MET cc_start: 0.6919 (mtm) cc_final: 0.6676 (mtt) REVERT: D 203 SER cc_start: 0.8647 (t) cc_final: 0.8010 (p) REVERT: D 225 ASP cc_start: 0.8138 (m-30) cc_final: 0.7926 (m-30) REVERT: D 457 LYS cc_start: 0.7915 (tttt) cc_final: 0.7417 (ttpp) REVERT: E 85 ASP cc_start: 0.7894 (p0) cc_final: 0.7686 (p0) outliers start: 59 outliers final: 50 residues processed: 263 average time/residue: 0.3084 time to fit residues: 111.6224 Evaluate side-chains 253 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 159 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14150 Z= 0.195 Angle : 0.523 9.590 19195 Z= 0.276 Chirality : 0.044 0.299 2210 Planarity : 0.004 0.041 2330 Dihedral : 6.480 89.375 2115 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.70 % Allowed : 10.17 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1640 helix: 1.50 (0.22), residues: 600 sheet: 0.89 (0.25), residues: 420 loop : -0.07 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 128 HIS 0.004 0.001 HIS D 254 PHE 0.012 0.001 PHE A 282 TYR 0.019 0.002 TYR E 362 ARG 0.004 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 199 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7301 (ptp90) REVERT: C 88 MET cc_start: 0.8864 (mtm) cc_final: 0.8636 (mtt) REVERT: C 115 ASP cc_start: 0.7914 (m-30) cc_final: 0.7699 (m-30) REVERT: C 170 ASP cc_start: 0.8176 (p0) cc_final: 0.7770 (p0) REVERT: C 298 LEU cc_start: 0.8150 (tp) cc_final: 0.7944 (tt) REVERT: C 457 LYS cc_start: 0.7867 (tttt) cc_final: 0.7354 (ttpp) REVERT: D 158 MET cc_start: 0.7983 (mmm) cc_final: 0.7740 (mmm) REVERT: D 170 ASP cc_start: 0.8138 (p0) cc_final: 0.7583 (p0) REVERT: D 185 LYS cc_start: 0.8254 (mttp) cc_final: 0.7981 (mtpp) REVERT: D 203 SER cc_start: 0.8781 (t) cc_final: 0.7950 (p) REVERT: D 457 LYS cc_start: 0.7849 (tttt) cc_final: 0.7359 (ttpp) REVERT: E 148 ARG cc_start: 0.7697 (ptt-90) cc_final: 0.7365 (ptt90) REVERT: E 335 MET cc_start: 0.5475 (tpt) cc_final: 0.5159 (tmm) outliers start: 55 outliers final: 49 residues processed: 238 average time/residue: 0.3509 time to fit residues: 114.5052 Evaluate side-chains 243 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14150 Z= 0.229 Angle : 0.528 6.480 19195 Z= 0.282 Chirality : 0.045 0.274 2210 Planarity : 0.004 0.039 2330 Dihedral : 6.141 84.048 2115 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.31 % Allowed : 10.17 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 0.98 (0.20), residues: 1640 helix: 1.43 (0.21), residues: 600 sheet: 0.87 (0.25), residues: 415 loop : -0.18 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.005 0.001 HIS E 254 PHE 0.012 0.001 PHE E 205 TYR 0.020 0.002 TYR E 362 ARG 0.004 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 201 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7759 (ptp90) cc_final: 0.7295 (ptp90) REVERT: B 265 THR cc_start: 0.7635 (p) cc_final: 0.7420 (p) REVERT: B 308 ARG cc_start: 0.7067 (mtm-85) cc_final: 0.6762 (mtp180) REVERT: C 88 MET cc_start: 0.8865 (mtm) cc_final: 0.8660 (mtt) REVERT: C 298 LEU cc_start: 0.8158 (tp) cc_final: 0.7953 (tt) REVERT: D 158 MET cc_start: 0.8035 (mmm) cc_final: 0.7710 (mmm) REVERT: D 185 LYS cc_start: 0.8288 (mttp) cc_final: 0.7999 (mtpp) REVERT: D 203 SER cc_start: 0.8773 (t) cc_final: 0.7991 (p) REVERT: D 225 ASP cc_start: 0.8107 (m-30) cc_final: 0.7895 (m-30) REVERT: D 457 LYS cc_start: 0.7930 (tttt) cc_final: 0.7427 (ttpp) outliers start: 64 outliers final: 56 residues processed: 248 average time/residue: 0.3131 time to fit residues: 106.9599 Evaluate side-chains 257 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 201 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 159 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14150 Z= 0.178 Angle : 0.497 7.266 19195 Z= 0.264 Chirality : 0.043 0.253 2210 Planarity : 0.004 0.043 2330 Dihedral : 5.738 79.822 2115 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.84 % Allowed : 10.98 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.06 (0.21), residues: 1640 helix: 1.54 (0.22), residues: 600 sheet: 0.86 (0.25), residues: 420 loop : -0.15 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 128 HIS 0.004 0.001 HIS C 254 PHE 0.011 0.001 PHE B 282 TYR 0.018 0.001 TYR E 362 ARG 0.003 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 202 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.7181 (mtpt) cc_final: 0.6907 (ttpt) REVERT: B 308 ARG cc_start: 0.7064 (mtm-85) cc_final: 0.6752 (mtp180) REVERT: B 335 MET cc_start: 0.6369 (tpt) cc_final: 0.5801 (tmm) REVERT: B 375 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.7052 (ttpt) REVERT: C 88 MET cc_start: 0.8854 (mtm) cc_final: 0.8649 (mtt) REVERT: C 457 LYS cc_start: 0.7882 (tttt) cc_final: 0.7324 (ttpp) REVERT: D 158 MET cc_start: 0.8036 (mmm) cc_final: 0.7734 (mmm) REVERT: D 185 LYS cc_start: 0.8259 (mttp) cc_final: 0.7949 (mtpp) REVERT: D 203 SER cc_start: 0.8740 (t) cc_final: 0.7951 (p) REVERT: D 457 LYS cc_start: 0.7900 (tttt) cc_final: 0.7397 (ttpp) REVERT: E 148 ARG cc_start: 0.7813 (ptt-90) cc_final: 0.7492 (ptt90) outliers start: 57 outliers final: 53 residues processed: 243 average time/residue: 0.3194 time to fit residues: 106.0831 Evaluate side-chains 254 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 200 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14150 Z= 0.199 Angle : 0.538 10.271 19195 Z= 0.279 Chirality : 0.052 1.273 2210 Planarity : 0.004 0.047 2330 Dihedral : 5.913 73.824 2115 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 4.44 % Allowed : 11.18 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.04 (0.21), residues: 1640 helix: 1.56 (0.21), residues: 600 sheet: 0.83 (0.25), residues: 420 loop : -0.19 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.004 0.001 HIS D 254 PHE 0.011 0.001 PHE E 205 TYR 0.018 0.001 TYR E 362 ARG 0.003 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 205 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 SER cc_start: 0.8293 (t) cc_final: 0.7985 (t) REVERT: A 375 LYS cc_start: 0.7162 (mtpt) cc_final: 0.6904 (ttpt) REVERT: B 308 ARG cc_start: 0.7063 (mtm-85) cc_final: 0.6748 (mtp180) REVERT: B 375 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.7008 (ttpt) REVERT: C 457 LYS cc_start: 0.7888 (tttt) cc_final: 0.7334 (ttpp) REVERT: D 158 MET cc_start: 0.8060 (mmm) cc_final: 0.7749 (mmm) REVERT: D 185 LYS cc_start: 0.8298 (mttp) cc_final: 0.7981 (mtpp) REVERT: D 203 SER cc_start: 0.8740 (t) cc_final: 0.7955 (p) REVERT: D 457 LYS cc_start: 0.7902 (tttt) cc_final: 0.7402 (ttpp) outliers start: 66 outliers final: 58 residues processed: 252 average time/residue: 0.3131 time to fit residues: 108.2000 Evaluate side-chains 263 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 204 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 144 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14150 Z= 0.227 Angle : 0.553 12.852 19195 Z= 0.285 Chirality : 0.052 1.229 2210 Planarity : 0.004 0.042 2330 Dihedral : 5.705 64.771 2115 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.24 % Allowed : 11.72 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 0.98 (0.20), residues: 1640 helix: 1.51 (0.21), residues: 600 sheet: 0.80 (0.25), residues: 420 loop : -0.22 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.004 0.001 HIS E 254 PHE 0.011 0.001 PHE E 205 TYR 0.019 0.002 TYR E 362 ARG 0.003 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 SER cc_start: 0.8308 (t) cc_final: 0.7990 (t) REVERT: A 375 LYS cc_start: 0.7203 (mtpt) cc_final: 0.6952 (ttpt) REVERT: B 308 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6746 (mtp180) REVERT: B 335 MET cc_start: 0.6223 (tpt) cc_final: 0.5568 (tmm) REVERT: B 375 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7022 (ttpt) REVERT: C 108 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8062 (mp) REVERT: C 235 ASP cc_start: 0.7431 (m-30) cc_final: 0.7209 (t0) REVERT: D 158 MET cc_start: 0.8090 (mmm) cc_final: 0.7764 (mmm) REVERT: D 185 LYS cc_start: 0.8311 (mttp) cc_final: 0.7994 (mtpp) REVERT: D 203 SER cc_start: 0.8732 (t) cc_final: 0.7955 (p) REVERT: D 225 ASP cc_start: 0.8144 (m-30) cc_final: 0.7936 (m-30) REVERT: D 337 ARG cc_start: 0.7274 (mtm180) cc_final: 0.6965 (mtt180) REVERT: D 457 LYS cc_start: 0.7946 (tttt) cc_final: 0.7434 (ttpp) outliers start: 63 outliers final: 58 residues processed: 255 average time/residue: 0.3056 time to fit residues: 107.6371 Evaluate side-chains 265 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 205 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14150 Z= 0.297 Angle : 0.578 9.260 19195 Z= 0.304 Chirality : 0.048 0.726 2210 Planarity : 0.004 0.042 2330 Dihedral : 5.813 56.714 2115 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.24 % Allowed : 11.92 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 0.79 (0.20), residues: 1640 helix: 1.36 (0.21), residues: 600 sheet: 0.75 (0.25), residues: 415 loop : -0.38 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.006 0.001 HIS E 254 PHE 0.014 0.002 PHE C 159 TYR 0.020 0.002 TYR D 362 ARG 0.004 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 205 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 SER cc_start: 0.8331 (t) cc_final: 0.8015 (t) REVERT: A 375 LYS cc_start: 0.7248 (mtpt) cc_final: 0.7006 (ttpt) REVERT: B 308 ARG cc_start: 0.7046 (mtm-85) cc_final: 0.6731 (mtp180) REVERT: B 375 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7094 (ttpt) REVERT: C 88 MET cc_start: 0.8846 (mtt) cc_final: 0.8496 (mtt) REVERT: C 108 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8058 (mp) REVERT: C 235 ASP cc_start: 0.7377 (m-30) cc_final: 0.7160 (t0) REVERT: D 158 MET cc_start: 0.8129 (mmm) cc_final: 0.7795 (mmm) REVERT: D 203 SER cc_start: 0.8733 (t) cc_final: 0.7973 (p) REVERT: D 337 ARG cc_start: 0.7295 (mtm180) cc_final: 0.6989 (mtt180) REVERT: E 148 ARG cc_start: 0.7665 (ptt-90) cc_final: 0.7460 (ptt90) REVERT: E 174 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7671 (t0) REVERT: E 375 LYS cc_start: 0.7263 (mtpt) cc_final: 0.6957 (ttpt) outliers start: 63 outliers final: 57 residues processed: 247 average time/residue: 0.3001 time to fit residues: 102.4540 Evaluate side-chains 265 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 205 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14150 Z= 0.265 Angle : 0.554 8.166 19195 Z= 0.293 Chirality : 0.047 0.647 2210 Planarity : 0.004 0.042 2330 Dihedral : 5.438 44.107 2115 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.97 % Allowed : 12.19 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 0.75 (0.20), residues: 1640 helix: 1.37 (0.21), residues: 600 sheet: 0.69 (0.25), residues: 415 loop : -0.41 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.005 0.001 HIS E 254 PHE 0.013 0.001 PHE C 159 TYR 0.018 0.002 TYR E 362 ARG 0.004 0.000 ARG C 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 204 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 SER cc_start: 0.8332 (t) cc_final: 0.8028 (t) REVERT: A 375 LYS cc_start: 0.7232 (mtpt) cc_final: 0.6985 (ttpt) REVERT: B 308 ARG cc_start: 0.7035 (mtm-85) cc_final: 0.6710 (mtp180) REVERT: B 375 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7134 (ttpt) REVERT: C 108 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8063 (mp) REVERT: D 203 SER cc_start: 0.8734 (t) cc_final: 0.7988 (p) REVERT: D 337 ARG cc_start: 0.7300 (mtm180) cc_final: 0.6932 (mtt180) REVERT: E 148 ARG cc_start: 0.7667 (ptt-90) cc_final: 0.7461 (ptt90) REVERT: E 174 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7674 (t0) REVERT: E 375 LYS cc_start: 0.7344 (mtpt) cc_final: 0.7079 (ttpt) outliers start: 59 outliers final: 56 residues processed: 243 average time/residue: 0.3109 time to fit residues: 104.2478 Evaluate side-chains 263 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 204 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 SER Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 246 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 24 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.142966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120098 restraints weight = 15402.287| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.00 r_work: 0.3159 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14150 Z= 0.161 Angle : 0.495 7.977 19195 Z= 0.260 Chirality : 0.044 0.570 2210 Planarity : 0.004 0.040 2330 Dihedral : 4.933 39.467 2115 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.03 % Allowed : 13.27 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1640 helix: 1.65 (0.22), residues: 595 sheet: 0.86 (0.25), residues: 415 loop : -0.21 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.003 0.001 HIS C 254 PHE 0.012 0.001 PHE B 282 TYR 0.015 0.001 TYR B 362 ARG 0.004 0.000 ARG E 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3223.29 seconds wall clock time: 59 minutes 40.75 seconds (3580.75 seconds total)