Starting phenix.real_space_refine on Sat Feb 17 13:16:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/02_2024/6qfa_4542_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/02_2024/6qfa_4542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/02_2024/6qfa_4542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/02_2024/6qfa_4542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/02_2024/6qfa_4542_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qfa_4542/02_2024/6qfa_4542_updated.pdb" } resolution = 2.49 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 12130 2.51 5 N 3060 2.21 5 O 3465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 488": "NH1" <-> "NH2" Residue "O ARG 488": "NH1" <-> "NH2" Residue "N ARG 488": "NH1" <-> "NH2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "L ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18755 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "K" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "O" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "N" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "M" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "L" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "D" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "E" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "A" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2728 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 317} Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'HSM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.97, per 1000 atoms: 0.53 Number of scatterers: 18755 At special positions: 0 Unit cell: (143.38, 138.03, 126.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3465 8.00 N 3060 7.00 C 12130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS K 409 " - pdb=" SG CYS K 483 " distance=2.03 Simple disulfide: pdb=" SG CYS O 409 " - pdb=" SG CYS O 483 " distance=2.03 Simple disulfide: pdb=" SG CYS N 409 " - pdb=" SG CYS N 483 " distance=2.03 Simple disulfide: pdb=" SG CYS M 409 " - pdb=" SG CYS M 483 " distance=2.03 Simple disulfide: pdb=" SG CYS L 409 " - pdb=" SG CYS L 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 136 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " 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 ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 80 " " NAG B 501 " - " ASN B 80 " " NAG C 501 " - " ASN C 80 " " NAG D 501 " - " ASN D 80 " " NAG E 501 " - " ASN E 80 " " NAG F 1 " - " ASN B 149 " " NAG G 1 " - " ASN C 149 " " NAG H 1 " - " ASN D 149 " " NAG I 1 " - " ASN E 149 " " NAG J 1 " - " ASN A 149 " Time building additional restraints: 7.02 Conformation dependent library (CDL) restraints added in 3.2 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 30 sheets defined 28.4% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.581A pdb=" N ASP B 89 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.687A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.549A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP B 241 " --> pdb=" O TRP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 271 removed outlier: 3.841A pdb=" N THR B 271 " --> pdb=" O HIS B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 446 removed outlier: 4.108A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'K' and resid 496 through 498 No H-bonds generated for 'chain 'K' and resid 496 through 498' Processing helix chain 'O' and resid 496 through 498 No H-bonds generated for 'chain 'O' and resid 496 through 498' Processing helix chain 'N' and resid 496 through 498 No H-bonds generated for 'chain 'N' and resid 496 through 498' Processing helix chain 'M' and resid 496 through 498 No H-bonds generated for 'chain 'M' and resid 496 through 498' Processing helix chain 'L' and resid 496 through 498 No H-bonds generated for 'chain 'L' and resid 496 through 498' Processing helix chain 'C' and resid 10 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.580A pdb=" N ASP C 89 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.790A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 241 removed outlier: 3.549A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.853A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR C 299 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 446 removed outlier: 4.108A pdb=" N ILE C 429 " --> pdb=" O ARG C 425 " (cutoff:3.500A) Proline residue: C 432 - end of helix Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.580A pdb=" N ASP D 89 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.687A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 241 removed outlier: 3.549A pdb=" N TRP D 237 " --> pdb=" O THR D 233 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE D 240 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP D 241 " --> pdb=" O TRP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 271 removed outlier: 3.582A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR D 271 " --> pdb=" O HIS D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 446 removed outlier: 4.108A pdb=" N ILE D 429 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Proline residue: D 432 - end of helix Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.580A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.687A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 241 removed outlier: 3.550A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 removed outlier: 3.576A pdb=" N GLU E 270 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR E 271 " --> pdb=" O HIS E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 446 removed outlier: 4.109A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.580A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.688A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 removed outlier: 3.550A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.587A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 removed outlier: 3.579A pdb=" N LEU A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 446 removed outlier: 4.109A pdb=" N ILE A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.239A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B 190 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS B 215 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE B 188 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 101 through 106 removed outlier: 6.873A pdb=" N THR B 133 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER B 104 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 131 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 2 through 7 Processing sheet with id= E, first strand: chain 'K' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR K 506 " --> pdb=" O TYR K 481 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL K 480 " --> pdb=" O GLN K 426 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE K 420 " --> pdb=" O LYS K 486 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG K 425 " --> pdb=" O PHE K 434 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE K 434 " --> pdb=" O ARG K 425 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 484 through 486 removed outlier: 3.897A pdb=" N TYR K 501 " --> pdb=" O ALA K 485 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'O' and resid 2 through 7 Processing sheet with id= H, first strand: chain 'O' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR O 506 " --> pdb=" O TYR O 481 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL O 480 " --> pdb=" O GLN O 426 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE O 420 " --> pdb=" O LYS O 486 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG O 425 " --> pdb=" O PHE O 434 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE O 434 " --> pdb=" O ARG O 425 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'O' and resid 484 through 486 removed outlier: 3.896A pdb=" N TYR O 501 " --> pdb=" O ALA O 485 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 2 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR N 506 " --> pdb=" O TYR N 481 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL N 480 " --> pdb=" O GLN N 426 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE N 420 " --> pdb=" O LYS N 486 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG N 425 " --> pdb=" O PHE N 434 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE N 434 " --> pdb=" O ARG N 425 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 484 through 486 removed outlier: 3.897A pdb=" N TYR N 501 " --> pdb=" O ALA N 485 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'M' and resid 2 through 7 Processing sheet with id= N, first strand: chain 'M' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR M 506 " --> pdb=" O TYR M 481 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL M 480 " --> pdb=" O GLN M 426 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 420 " --> pdb=" O LYS M 486 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG M 425 " --> pdb=" O PHE M 434 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE M 434 " --> pdb=" O ARG M 425 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'M' and resid 484 through 486 removed outlier: 3.897A pdb=" N TYR M 501 " --> pdb=" O ALA M 485 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 2 through 7 Processing sheet with id= Q, first strand: chain 'L' and resid 506 through 508 removed outlier: 3.648A pdb=" N THR L 506 " --> pdb=" O TYR L 481 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL L 480 " --> pdb=" O GLN L 426 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE L 420 " --> pdb=" O LYS L 486 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG L 425 " --> pdb=" O PHE L 434 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE L 434 " --> pdb=" O ARG L 425 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 484 through 486 removed outlier: 3.897A pdb=" N TYR L 501 " --> pdb=" O ALA L 485 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.274A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG C 68 " --> pdb=" O CYS C 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU C 190 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.851A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.272A pdb=" N VAL D 36 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N TYR D 167 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL D 38 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS D 37 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG D 68 " --> pdb=" O CYS D 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR D 58 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE D 116 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER D 156 " --> pdb=" O PRO D 206 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU D 190 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS D 215 " --> pdb=" O ILE D 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE D 188 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 101 through 106 removed outlier: 6.890A pdb=" N THR D 133 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 104 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR D 131 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.275A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU E 190 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS E 215 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE E 188 " --> pdb=" O LYS E 215 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 101 through 106 removed outlier: 6.868A pdb=" N THR E 133 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER E 104 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR E 131 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.270A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG A 68 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.632A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU A 190 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.852A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) 792 hydrogen bonds defined for protein. 2286 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: 6.25 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2983 1.32 - 1.45: 5751 1.45 - 1.57: 10336 1.57 - 1.69: 0 1.69 - 1.81: 170 Bond restraints: 19240 Sorted by residual: bond pdb=" C PRO C 34 " pdb=" O PRO C 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.40e+01 bond pdb=" C PRO A 34 " pdb=" O PRO A 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.40e+01 bond pdb=" C PRO B 34 " pdb=" O PRO B 34 " ideal model delta sigma weight residual 1.243 1.202 0.042 8.50e-03 1.38e+04 2.38e+01 bond pdb=" C PRO E 34 " pdb=" O PRO E 34 " ideal model delta sigma weight residual 1.243 1.202 0.041 8.50e-03 1.38e+04 2.33e+01 bond pdb=" C PRO D 34 " pdb=" O PRO D 34 " ideal model delta sigma weight residual 1.243 1.202 0.041 8.50e-03 1.38e+04 2.31e+01 ... (remaining 19235 not shown) Histogram of bond angle deviations from ideal: 99.33 - 106.27: 509 106.27 - 113.22: 10181 113.22 - 120.16: 7168 120.16 - 127.11: 8079 127.11 - 134.05: 218 Bond angle restraints: 26155 Sorted by residual: angle pdb=" C ARG C 269 " pdb=" N GLU C 270 " pdb=" CA GLU C 270 " ideal model delta sigma weight residual 120.28 125.64 -5.36 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C ARG B 269 " pdb=" N GLU B 270 " pdb=" CA GLU B 270 " ideal model delta sigma weight residual 120.28 125.63 -5.35 1.44e+00 4.82e-01 1.38e+01 angle pdb=" C LEU D 223 " pdb=" N GLN D 224 " pdb=" CA GLN D 224 " ideal model delta sigma weight residual 120.29 125.01 -4.72 1.42e+00 4.96e-01 1.11e+01 angle pdb=" C LEU E 223 " pdb=" N GLN E 224 " pdb=" CA GLN E 224 " ideal model delta sigma weight residual 120.29 124.99 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" N GLN B 224 " pdb=" CA GLN B 224 " pdb=" C GLN B 224 " ideal model delta sigma weight residual 111.36 114.96 -3.60 1.09e+00 8.42e-01 1.09e+01 ... (remaining 26150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 11100 20.58 - 41.16: 379 41.16 - 61.74: 51 61.74 - 82.32: 35 82.32 - 102.89: 25 Dihedral angle restraints: 11590 sinusoidal: 4945 harmonic: 6645 Sorted by residual: dihedral pdb=" CA SER E 46 " pdb=" C SER E 46 " pdb=" N ILE E 47 " pdb=" CA ILE E 47 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER A 46 " pdb=" C SER A 46 " pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta harmonic sigma weight residual 180.00 160.87 19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER B 46 " pdb=" C SER B 46 " pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 11587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2317 0.059 - 0.119: 467 0.119 - 0.178: 153 0.178 - 0.237: 21 0.237 - 0.296: 7 Chirality restraints: 2965 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.18e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.14e+02 ... (remaining 2962 not shown) Planarity restraints: 3245 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 227 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 228 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 227 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO C 228 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 227 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO A 228 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.031 5.00e-02 4.00e+02 ... (remaining 3242 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 136 2.56 - 3.14: 13329 3.14 - 3.73: 29316 3.73 - 4.31: 45368 4.31 - 4.90: 71708 Nonbonded interactions: 159857 Sorted by model distance: nonbonded pdb=" OD1 ASP E 101 " pdb=" OG SER E 104 " model vdw 1.973 2.440 nonbonded pdb=" OD1 ASP C 101 " pdb=" OG SER C 104 " model vdw 1.976 2.440 nonbonded pdb=" NH1 ARG E 269 " pdb=" OD1 ASP E 282 " model vdw 2.140 2.520 nonbonded pdb=" NH1 ARG D 269 " pdb=" OD1 ASP D 282 " model vdw 2.145 2.520 nonbonded pdb=" NH1 ARG A 269 " pdb=" OD1 ASP A 282 " model vdw 2.150 2.520 ... (remaining 159852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.040 Extract box with map and model: 4.410 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 50.170 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 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 : 0.005 0.045 19240 Z= 0.344 Angle : 0.800 6.568 26155 Z= 0.497 Chirality : 0.058 0.296 2965 Planarity : 0.005 0.056 3235 Dihedral : 12.652 102.894 7330 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -2.14 (0.16), residues: 2240 helix: -3.79 (0.11), residues: 615 sheet: 0.39 (0.19), residues: 670 loop : -0.92 (0.18), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 426 HIS 0.003 0.001 HIS A 119 PHE 0.011 0.002 PHE D 105 TYR 0.020 0.002 TYR D 299 ARG 0.004 0.000 ARG C 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.951 Fit side-chains REVERT: B 18 LYS cc_start: 0.7636 (tttt) cc_final: 0.7200 (tmmt) REVERT: B 137 MET cc_start: 0.8335 (mmp) cc_final: 0.8078 (mmp) REVERT: B 179 GLU cc_start: 0.8062 (pm20) cc_final: 0.7826 (pm20) REVERT: B 261 MET cc_start: 0.8936 (mmt) cc_final: 0.8675 (tpp) REVERT: K 425 ARG cc_start: 0.7749 (ptt180) cc_final: 0.7547 (ptt180) REVERT: N 447 TYR cc_start: 0.8366 (m-80) cc_final: 0.7743 (m-80) REVERT: C 18 LYS cc_start: 0.7631 (tttt) cc_final: 0.7125 (tmmt) REVERT: C 52 GLU cc_start: 0.8573 (mp0) cc_final: 0.8340 (mp0) REVERT: C 90 GLN cc_start: 0.8795 (mt0) cc_final: 0.8582 (mp10) REVERT: C 261 MET cc_start: 0.9027 (mmt) cc_final: 0.8641 (mmm) REVERT: C 298 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8626 (tm-30) REVERT: C 440 LEU cc_start: 0.8282 (tp) cc_final: 0.8033 (tt) REVERT: D 18 LYS cc_start: 0.7585 (tttt) cc_final: 0.7025 (tmmt) REVERT: D 48 ASP cc_start: 0.7187 (m-30) cc_final: 0.6931 (m-30) REVERT: D 52 GLU cc_start: 0.8570 (mp0) cc_final: 0.8326 (mp0) REVERT: D 115 MET cc_start: 0.8581 (ttm) cc_final: 0.8375 (tmm) REVERT: D 243 ASN cc_start: 0.7858 (t0) cc_final: 0.7219 (t0) REVERT: D 244 TYR cc_start: 0.7784 (p90) cc_final: 0.7551 (p90) REVERT: D 304 TYR cc_start: 0.8847 (t80) cc_final: 0.8469 (t80) REVERT: E 14 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6858 (mt-10) REVERT: E 56 ASP cc_start: 0.8763 (p0) cc_final: 0.8499 (p0) REVERT: E 90 GLN cc_start: 0.8783 (mt0) cc_final: 0.8466 (mp10) REVERT: E 115 MET cc_start: 0.8481 (ttm) cc_final: 0.7973 (tmm) REVERT: E 137 MET cc_start: 0.8428 (mmp) cc_final: 0.8017 (mmp) REVERT: E 215 LYS cc_start: 0.8619 (tttt) cc_final: 0.8390 (tptp) REVERT: E 243 ASN cc_start: 0.7594 (t0) cc_final: 0.7074 (t0) REVERT: E 244 TYR cc_start: 0.7806 (p90) cc_final: 0.7578 (p90) REVERT: E 245 ASP cc_start: 0.7627 (m-30) cc_final: 0.7320 (p0) REVERT: E 261 MET cc_start: 0.9010 (mmt) cc_final: 0.8764 (tpp) REVERT: E 283 MET cc_start: 0.8345 (mmm) cc_final: 0.8111 (mmm) REVERT: A 90 GLN cc_start: 0.8706 (mt0) cc_final: 0.8377 (mp10) REVERT: A 261 MET cc_start: 0.9017 (mmt) cc_final: 0.8742 (tpp) REVERT: A 283 MET cc_start: 0.8371 (mmm) cc_final: 0.8131 (mmm) REVERT: A 440 LEU cc_start: 0.8463 (tp) cc_final: 0.8190 (tt) outliers start: 0 outliers final: 2 residues processed: 353 average time/residue: 1.3060 time to fit residues: 517.9969 Evaluate side-chains 321 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 319 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 255 ILE Chi-restraints excluded: chain D residue 255 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 204 optimal weight: 0.3980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN B 90 GLN B 185 GLN C 243 ASN D 185 GLN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19240 Z= 0.183 Angle : 0.547 5.056 26155 Z= 0.296 Chirality : 0.044 0.149 2965 Planarity : 0.004 0.037 3235 Dihedral : 9.400 74.732 3174 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.32 % Allowed : 7.85 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2240 helix: -0.40 (0.18), residues: 610 sheet: 0.69 (0.20), residues: 655 loop : -0.46 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 426 HIS 0.003 0.001 HIS C 107 PHE 0.011 0.001 PHE K 424 TYR 0.023 0.002 TYR E 299 ARG 0.004 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 358 time to evaluate : 1.933 Fit side-chains REVERT: B 18 LYS cc_start: 0.7826 (tttt) cc_final: 0.7258 (tmmt) REVERT: B 70 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8234 (mttp) REVERT: B 137 MET cc_start: 0.8380 (mmp) cc_final: 0.7910 (mmp) REVERT: B 261 MET cc_start: 0.8952 (mmt) cc_final: 0.8734 (tpp) REVERT: K 415 THR cc_start: 0.8264 (m) cc_final: 0.7964 (t) REVERT: K 425 ARG cc_start: 0.7956 (ptt180) cc_final: 0.7755 (ptt180) REVERT: N 421 MET cc_start: 0.8796 (mmt) cc_final: 0.8503 (tpp) REVERT: N 447 TYR cc_start: 0.8407 (m-80) cc_final: 0.7887 (m-80) REVERT: L 482 TYR cc_start: 0.7697 (m-80) cc_final: 0.7416 (m-80) REVERT: C 18 LYS cc_start: 0.7537 (tttt) cc_final: 0.7150 (tmmt) REVERT: C 90 GLN cc_start: 0.8766 (mt0) cc_final: 0.8507 (mp10) REVERT: C 115 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7964 (tmm) REVERT: C 182 GLU cc_start: 0.8296 (mt-10) cc_final: 0.8077 (mt-10) REVERT: C 261 MET cc_start: 0.9070 (mmt) cc_final: 0.8588 (mmm) REVERT: C 285 LEU cc_start: 0.9125 (mt) cc_final: 0.8884 (mm) REVERT: C 440 LEU cc_start: 0.8495 (tp) cc_final: 0.8247 (tt) REVERT: D 18 LYS cc_start: 0.7469 (tttt) cc_final: 0.7073 (tmmt) REVERT: D 49 MET cc_start: 0.7503 (tmm) cc_final: 0.7244 (tmm) REVERT: D 52 GLU cc_start: 0.8567 (mp0) cc_final: 0.8323 (mp0) REVERT: D 165 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7297 (mm-30) REVERT: D 243 ASN cc_start: 0.7669 (t0) cc_final: 0.7152 (t0) REVERT: D 244 TYR cc_start: 0.7881 (p90) cc_final: 0.7534 (p90) REVERT: D 304 TYR cc_start: 0.8838 (t80) cc_final: 0.8532 (t80) REVERT: D 440 LEU cc_start: 0.8708 (tp) cc_final: 0.8419 (tt) REVERT: E 14 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6883 (mt-10) REVERT: E 18 LYS cc_start: 0.7543 (tttt) cc_final: 0.6915 (tmmt) REVERT: E 56 ASP cc_start: 0.8847 (p0) cc_final: 0.8601 (p0) REVERT: E 90 GLN cc_start: 0.8773 (mt0) cc_final: 0.8471 (mp10) REVERT: E 115 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7933 (tmm) REVERT: E 137 MET cc_start: 0.8370 (mmp) cc_final: 0.7987 (mmp) REVERT: E 165 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7541 (mm-30) REVERT: E 215 LYS cc_start: 0.8610 (tttt) cc_final: 0.8384 (tptp) REVERT: E 243 ASN cc_start: 0.7840 (t0) cc_final: 0.7319 (t0) REVERT: E 244 TYR cc_start: 0.7846 (p90) cc_final: 0.7606 (p90) REVERT: E 245 ASP cc_start: 0.7634 (m-30) cc_final: 0.7354 (p0) REVERT: E 283 MET cc_start: 0.8257 (mmm) cc_final: 0.7968 (mmm) REVERT: A 68 ARG cc_start: 0.8264 (tpp80) cc_final: 0.8015 (tpp80) REVERT: A 90 GLN cc_start: 0.8712 (mt0) cc_final: 0.8396 (mp10) REVERT: A 429 ILE cc_start: 0.8499 (pt) cc_final: 0.8296 (pp) REVERT: A 440 LEU cc_start: 0.8575 (tp) cc_final: 0.8340 (tt) outliers start: 26 outliers final: 16 residues processed: 364 average time/residue: 1.3235 time to fit residues: 539.5399 Evaluate side-chains 356 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 335 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain O residue 445 THR Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 6.9990 chunk 63 optimal weight: 0.0170 chunk 170 optimal weight: 6.9990 chunk 139 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 overall best weight: 2.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 185 GLN C 243 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 19240 Z= 0.307 Angle : 0.608 5.896 26155 Z= 0.325 Chirality : 0.047 0.153 2965 Planarity : 0.004 0.045 3235 Dihedral : 9.362 72.419 3172 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.03 % Allowed : 9.27 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.48 (0.17), residues: 2240 helix: 0.74 (0.20), residues: 615 sheet: 0.66 (0.20), residues: 665 loop : -0.08 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 426 HIS 0.006 0.001 HIS D 107 PHE 0.016 0.002 PHE C 221 TYR 0.032 0.002 TYR A 299 ARG 0.008 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 352 time to evaluate : 2.108 Fit side-chains REVERT: B 18 LYS cc_start: 0.7832 (tttt) cc_final: 0.7263 (tmmt) REVERT: B 70 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8365 (mttp) REVERT: B 137 MET cc_start: 0.8313 (mmp) cc_final: 0.8008 (mmp) REVERT: B 165 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: B 261 MET cc_start: 0.9006 (mmt) cc_final: 0.8796 (tpp) REVERT: B 268 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8363 (tp) REVERT: K 415 THR cc_start: 0.8301 (m) cc_final: 0.8027 (t) REVERT: K 447 TYR cc_start: 0.8416 (m-80) cc_final: 0.8137 (m-80) REVERT: N 415 THR cc_start: 0.8358 (m) cc_final: 0.7907 (t) REVERT: N 421 MET cc_start: 0.8826 (mmt) cc_final: 0.8531 (tpp) REVERT: N 447 TYR cc_start: 0.8406 (m-80) cc_final: 0.8181 (m-80) REVERT: N 457 ILE cc_start: 0.7509 (mt) cc_final: 0.7306 (mt) REVERT: L 425 ARG cc_start: 0.8066 (ptt180) cc_final: 0.7708 (ptt180) REVERT: C 18 LYS cc_start: 0.7660 (tttt) cc_final: 0.7253 (tmmt) REVERT: C 90 GLN cc_start: 0.8748 (mt0) cc_final: 0.8455 (mp10) REVERT: C 115 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8059 (tmm) REVERT: C 261 MET cc_start: 0.9093 (mmt) cc_final: 0.8654 (mmm) REVERT: C 298 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8758 (tm-30) REVERT: C 440 LEU cc_start: 0.8575 (tp) cc_final: 0.8344 (tt) REVERT: D 18 LYS cc_start: 0.7576 (tttt) cc_final: 0.7198 (tmmt) REVERT: D 49 MET cc_start: 0.7460 (tmm) cc_final: 0.7184 (tmm) REVERT: D 52 GLU cc_start: 0.8584 (mp0) cc_final: 0.8361 (mp0) REVERT: D 165 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7346 (mm-30) REVERT: D 243 ASN cc_start: 0.7760 (t0) cc_final: 0.7398 (t0) REVERT: D 244 TYR cc_start: 0.7978 (p90) cc_final: 0.7655 (p90) REVERT: D 440 LEU cc_start: 0.8736 (tp) cc_final: 0.8483 (tt) REVERT: E 14 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6823 (mt-10) REVERT: E 18 LYS cc_start: 0.7744 (tttt) cc_final: 0.7146 (tmmt) REVERT: E 56 ASP cc_start: 0.8908 (p0) cc_final: 0.8650 (p0) REVERT: E 90 GLN cc_start: 0.8772 (mt0) cc_final: 0.8459 (mp10) REVERT: E 115 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7976 (tmm) REVERT: E 137 MET cc_start: 0.8381 (mmp) cc_final: 0.8015 (mmp) REVERT: E 165 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: E 215 LYS cc_start: 0.8634 (tttt) cc_final: 0.8400 (tptp) REVERT: E 243 ASN cc_start: 0.7958 (t0) cc_final: 0.7478 (t0) REVERT: E 245 ASP cc_start: 0.7677 (m-30) cc_final: 0.7391 (p0) REVERT: A 90 GLN cc_start: 0.8738 (mt0) cc_final: 0.8377 (mp10) REVERT: A 429 ILE cc_start: 0.8585 (pt) cc_final: 0.8367 (pp) outliers start: 40 outliers final: 22 residues processed: 363 average time/residue: 1.3524 time to fit residues: 549.3380 Evaluate side-chains 367 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 338 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 194 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 113 ASN C 243 ASN D 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19240 Z= 0.268 Angle : 0.573 5.886 26155 Z= 0.307 Chirality : 0.046 0.151 2965 Planarity : 0.004 0.039 3235 Dihedral : 8.945 69.079 3170 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.28 % Allowed : 9.32 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.80 (0.17), residues: 2240 helix: 1.20 (0.21), residues: 615 sheet: 0.67 (0.19), residues: 665 loop : 0.11 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.004 0.001 HIS D 107 PHE 0.016 0.002 PHE A 98 TYR 0.029 0.002 TYR E 299 ARG 0.005 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 345 time to evaluate : 2.195 Fit side-chains REVERT: B 18 LYS cc_start: 0.7774 (tttt) cc_final: 0.7227 (tmmt) REVERT: B 70 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8458 (mptt) REVERT: B 137 MET cc_start: 0.8279 (mmp) cc_final: 0.8001 (mmp) REVERT: B 224 GLN cc_start: 0.8566 (tp40) cc_final: 0.8284 (tp-100) REVERT: B 261 MET cc_start: 0.9016 (mmt) cc_final: 0.8804 (tpp) REVERT: K 447 TYR cc_start: 0.8427 (m-80) cc_final: 0.8155 (m-80) REVERT: N 415 THR cc_start: 0.8213 (m) cc_final: 0.7833 (t) REVERT: L 482 TYR cc_start: 0.7620 (m-80) cc_final: 0.7321 (m-80) REVERT: C 18 LYS cc_start: 0.7639 (tttt) cc_final: 0.7235 (tmmt) REVERT: C 48 ASP cc_start: 0.7157 (m-30) cc_final: 0.6548 (m-30) REVERT: C 90 GLN cc_start: 0.8741 (mt0) cc_final: 0.8470 (mp10) REVERT: C 115 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8002 (tmm) REVERT: C 261 MET cc_start: 0.9069 (mmt) cc_final: 0.8630 (mmm) REVERT: C 285 LEU cc_start: 0.9013 (mt) cc_final: 0.8811 (mm) REVERT: C 298 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8783 (tm-30) REVERT: C 440 LEU cc_start: 0.8599 (tp) cc_final: 0.8352 (tt) REVERT: D 18 LYS cc_start: 0.7534 (tttt) cc_final: 0.7169 (tmmt) REVERT: D 49 MET cc_start: 0.7469 (tmm) cc_final: 0.7262 (tmm) REVERT: D 52 GLU cc_start: 0.8599 (mp0) cc_final: 0.8390 (mp0) REVERT: D 243 ASN cc_start: 0.7775 (t0) cc_final: 0.7434 (t0) REVERT: D 244 TYR cc_start: 0.7969 (p90) cc_final: 0.7659 (p90) REVERT: D 440 LEU cc_start: 0.8734 (tp) cc_final: 0.8514 (tt) REVERT: E 18 LYS cc_start: 0.7705 (tttt) cc_final: 0.7146 (tmmt) REVERT: E 48 ASP cc_start: 0.7120 (m-30) cc_final: 0.6487 (m-30) REVERT: E 56 ASP cc_start: 0.8896 (p0) cc_final: 0.8650 (p0) REVERT: E 115 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7948 (tmm) REVERT: E 165 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: E 215 LYS cc_start: 0.8617 (tttt) cc_final: 0.8391 (tptp) REVERT: E 243 ASN cc_start: 0.8063 (t0) cc_final: 0.7597 (t0) REVERT: E 245 ASP cc_start: 0.7770 (m-30) cc_final: 0.7464 (p0) REVERT: A 90 GLN cc_start: 0.8738 (mt0) cc_final: 0.8386 (mp10) REVERT: A 165 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7530 (mm-30) outliers start: 45 outliers final: 28 residues processed: 356 average time/residue: 1.3125 time to fit residues: 523.5076 Evaluate side-chains 368 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 335 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 445 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 195 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 113 ASN C 243 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19240 Z= 0.269 Angle : 0.574 5.926 26155 Z= 0.306 Chirality : 0.046 0.153 2965 Planarity : 0.004 0.039 3235 Dihedral : 8.869 68.236 3170 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.53 % Allowed : 9.47 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.93 (0.18), residues: 2240 helix: 1.41 (0.21), residues: 615 sheet: 0.69 (0.19), residues: 660 loop : 0.17 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.004 0.001 HIS D 107 PHE 0.016 0.002 PHE A 98 TYR 0.029 0.002 TYR E 299 ARG 0.005 0.001 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 348 time to evaluate : 2.102 Fit side-chains REVERT: B 18 LYS cc_start: 0.7717 (tttt) cc_final: 0.7197 (tmmt) REVERT: B 70 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8446 (mptt) REVERT: B 165 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: B 224 GLN cc_start: 0.8550 (tp40) cc_final: 0.8308 (tp-100) REVERT: B 268 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8298 (tp) REVERT: K 447 TYR cc_start: 0.8425 (m-80) cc_final: 0.8169 (m-80) REVERT: O 468 LEU cc_start: 0.6149 (tp) cc_final: 0.5795 (tp) REVERT: N 415 THR cc_start: 0.8091 (m) cc_final: 0.7785 (t) REVERT: L 482 TYR cc_start: 0.7595 (m-80) cc_final: 0.7327 (m-80) REVERT: C 18 LYS cc_start: 0.7671 (tttt) cc_final: 0.7240 (tmmt) REVERT: C 48 ASP cc_start: 0.7272 (m-30) cc_final: 0.6683 (m-30) REVERT: C 90 GLN cc_start: 0.8747 (mt0) cc_final: 0.8460 (mp10) REVERT: C 115 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7902 (tmm) REVERT: C 261 MET cc_start: 0.9093 (mmt) cc_final: 0.8594 (mmm) REVERT: C 285 LEU cc_start: 0.9006 (mt) cc_final: 0.8804 (mm) REVERT: D 18 LYS cc_start: 0.7524 (tttt) cc_final: 0.7170 (tmmt) REVERT: D 52 GLU cc_start: 0.8577 (mp0) cc_final: 0.8361 (mp0) REVERT: D 165 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7340 (mm-30) REVERT: D 243 ASN cc_start: 0.7744 (t0) cc_final: 0.7427 (t0) REVERT: D 244 TYR cc_start: 0.7969 (p90) cc_final: 0.7655 (p90) REVERT: D 440 LEU cc_start: 0.8748 (tp) cc_final: 0.8513 (tt) REVERT: E 18 LYS cc_start: 0.7697 (tttt) cc_final: 0.7132 (tmmt) REVERT: E 48 ASP cc_start: 0.7195 (m-30) cc_final: 0.6529 (m-30) REVERT: E 56 ASP cc_start: 0.8891 (p0) cc_final: 0.8651 (p0) REVERT: E 115 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7979 (tmm) REVERT: E 215 LYS cc_start: 0.8620 (tttt) cc_final: 0.8393 (tptp) REVERT: E 243 ASN cc_start: 0.8073 (t0) cc_final: 0.7618 (t0) REVERT: E 245 ASP cc_start: 0.7733 (m-30) cc_final: 0.7471 (p0) REVERT: A 90 GLN cc_start: 0.8741 (mt0) cc_final: 0.8367 (mp10) REVERT: A 165 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7518 (mm-30) outliers start: 50 outliers final: 28 residues processed: 362 average time/residue: 1.3162 time to fit residues: 533.9851 Evaluate side-chains 371 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 336 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 445 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 217 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 41 ASN C 243 ASN C 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 19240 Z= 0.439 Angle : 0.685 6.786 26155 Z= 0.363 Chirality : 0.051 0.162 2965 Planarity : 0.005 0.058 3235 Dihedral : 9.680 73.614 3170 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.84 % Allowed : 9.67 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.87 (0.18), residues: 2240 helix: 1.23 (0.21), residues: 615 sheet: 0.72 (0.19), residues: 650 loop : 0.18 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 426 HIS 0.005 0.001 HIS D 107 PHE 0.020 0.002 PHE A 98 TYR 0.033 0.003 TYR D 299 ARG 0.010 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 334 time to evaluate : 2.141 Fit side-chains REVERT: B 18 LYS cc_start: 0.7649 (tttt) cc_final: 0.7196 (tmmt) REVERT: B 70 LYS cc_start: 0.8748 (mttp) cc_final: 0.8495 (mptt) REVERT: B 165 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: B 224 GLN cc_start: 0.8597 (tp40) cc_final: 0.8361 (tp-100) REVERT: B 268 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8360 (tp) REVERT: K 447 TYR cc_start: 0.8456 (m-80) cc_final: 0.8175 (m-80) REVERT: N 415 THR cc_start: 0.8205 (m) cc_final: 0.7882 (t) REVERT: L 425 ARG cc_start: 0.8057 (ptt180) cc_final: 0.7839 (ptt180) REVERT: C 18 LYS cc_start: 0.7669 (tttt) cc_final: 0.7239 (tmmt) REVERT: C 48 ASP cc_start: 0.7378 (m-30) cc_final: 0.6719 (m-30) REVERT: C 90 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8494 (mp10) REVERT: C 115 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8023 (tmm) REVERT: C 261 MET cc_start: 0.9121 (mmt) cc_final: 0.8688 (mmm) REVERT: C 285 LEU cc_start: 0.8952 (mt) cc_final: 0.8743 (mm) REVERT: D 18 LYS cc_start: 0.7657 (tttt) cc_final: 0.7298 (tmmt) REVERT: D 68 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8142 (tpp80) REVERT: D 90 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: D 165 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: D 243 ASN cc_start: 0.8038 (t0) cc_final: 0.7696 (t0) REVERT: D 244 TYR cc_start: 0.8066 (p90) cc_final: 0.7813 (p90) REVERT: D 440 LEU cc_start: 0.8765 (tp) cc_final: 0.8514 (tt) REVERT: E 18 LYS cc_start: 0.7707 (tttt) cc_final: 0.7107 (tmmt) REVERT: E 48 ASP cc_start: 0.7218 (m-30) cc_final: 0.6562 (m-30) REVERT: E 56 ASP cc_start: 0.8898 (p0) cc_final: 0.8665 (p0) REVERT: E 115 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8059 (tmm) REVERT: E 165 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: E 215 LYS cc_start: 0.8641 (tttt) cc_final: 0.8400 (tptp) REVERT: E 243 ASN cc_start: 0.8148 (t0) cc_final: 0.7736 (t0) REVERT: E 245 ASP cc_start: 0.7795 (m-30) cc_final: 0.7514 (p0) REVERT: A 90 GLN cc_start: 0.8806 (mt0) cc_final: 0.8463 (mp10) REVERT: A 165 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: A 190 GLU cc_start: 0.8549 (tt0) cc_final: 0.8257 (tt0) outliers start: 56 outliers final: 34 residues processed: 354 average time/residue: 1.3460 time to fit residues: 532.9512 Evaluate side-chains 379 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 335 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain K residue 470 MET Chi-restraints excluded: chain O residue 445 THR Chi-restraints excluded: chain O residue 470 MET Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain N residue 445 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 90 GLN Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 165 GLU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 243 ASN B 265 ASN C 243 ASN C 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19240 Z= 0.169 Angle : 0.522 7.402 26155 Z= 0.278 Chirality : 0.044 0.158 2965 Planarity : 0.003 0.036 3235 Dihedral : 8.497 65.914 3170 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.57 % Allowed : 11.09 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 1.01 (0.18), residues: 2240 helix: 1.62 (0.22), residues: 615 sheet: 0.72 (0.19), residues: 635 loop : 0.14 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 440 HIS 0.002 0.000 HIS E 119 PHE 0.014 0.001 PHE A 98 TYR 0.026 0.001 TYR E 299 ARG 0.005 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 349 time to evaluate : 2.079 Fit side-chains REVERT: B 18 LYS cc_start: 0.7678 (tttt) cc_final: 0.7158 (tmmt) REVERT: B 70 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8421 (mmtt) REVERT: B 224 GLN cc_start: 0.8610 (tp40) cc_final: 0.8379 (tp-100) REVERT: K 447 TYR cc_start: 0.8413 (m-80) cc_final: 0.8097 (m-80) REVERT: O 468 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5621 (tp) REVERT: N 415 THR cc_start: 0.8000 (m) cc_final: 0.7706 (t) REVERT: C 18 LYS cc_start: 0.7662 (tttt) cc_final: 0.7239 (tmmt) REVERT: C 48 ASP cc_start: 0.7346 (m-30) cc_final: 0.6705 (m-30) REVERT: C 90 GLN cc_start: 0.8747 (mt0) cc_final: 0.8490 (mp10) REVERT: C 115 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8005 (tmm) REVERT: C 261 MET cc_start: 0.9058 (mmt) cc_final: 0.8607 (mmm) REVERT: D 18 LYS cc_start: 0.7584 (tttt) cc_final: 0.7217 (tmmt) REVERT: D 59 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8802 (tt) REVERT: D 243 ASN cc_start: 0.7750 (t0) cc_final: 0.7422 (t0) REVERT: D 244 TYR cc_start: 0.7929 (p90) cc_final: 0.7665 (p90) REVERT: D 440 LEU cc_start: 0.8761 (tp) cc_final: 0.8540 (tt) REVERT: E 18 LYS cc_start: 0.7821 (tttt) cc_final: 0.7231 (tmmt) REVERT: E 48 ASP cc_start: 0.7168 (m-30) cc_final: 0.6506 (m-30) REVERT: E 56 ASP cc_start: 0.8868 (p0) cc_final: 0.8633 (p0) REVERT: E 115 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7961 (tmm) REVERT: E 215 LYS cc_start: 0.8609 (tttt) cc_final: 0.8401 (tptp) REVERT: E 243 ASN cc_start: 0.8058 (t0) cc_final: 0.7613 (t0) REVERT: A 90 GLN cc_start: 0.8753 (mt0) cc_final: 0.8380 (mp10) REVERT: A 190 GLU cc_start: 0.8455 (tt0) cc_final: 0.8166 (tt0) outliers start: 31 outliers final: 19 residues processed: 360 average time/residue: 1.3481 time to fit residues: 542.9791 Evaluate side-chains 361 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 337 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 0.0980 chunk 86 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 243 ASN C 265 ASN E 185 GLN A 41 ASN A 243 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19240 Z= 0.303 Angle : 0.599 7.802 26155 Z= 0.317 Chirality : 0.047 0.157 2965 Planarity : 0.004 0.042 3235 Dihedral : 8.846 67.302 3170 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.48 % Allowed : 10.63 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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 (0.18), residues: 2240 helix: 1.48 (0.21), residues: 620 sheet: 0.58 (0.19), residues: 685 loop : 0.29 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 426 HIS 0.004 0.001 HIS D 107 PHE 0.019 0.002 PHE A 98 TYR 0.029 0.002 TYR A 299 ARG 0.006 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 343 time to evaluate : 2.197 Fit side-chains REVERT: B 18 LYS cc_start: 0.7679 (tttt) cc_final: 0.7141 (tmmt) REVERT: B 70 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8470 (mmtt) REVERT: B 165 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: B 224 GLN cc_start: 0.8646 (tp40) cc_final: 0.8421 (tp-100) REVERT: K 447 TYR cc_start: 0.8429 (m-80) cc_final: 0.8121 (m-80) REVERT: O 468 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5717 (tp) REVERT: N 415 THR cc_start: 0.8013 (m) cc_final: 0.7720 (t) REVERT: C 18 LYS cc_start: 0.7673 (tttt) cc_final: 0.7246 (tmmt) REVERT: C 48 ASP cc_start: 0.7383 (m-30) cc_final: 0.6723 (m-30) REVERT: C 90 GLN cc_start: 0.8762 (mt0) cc_final: 0.8476 (mp10) REVERT: C 115 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8074 (tmm) REVERT: C 261 MET cc_start: 0.9074 (mmt) cc_final: 0.8685 (mmm) REVERT: C 267 HIS cc_start: 0.7237 (m170) cc_final: 0.6894 (m170) REVERT: D 18 LYS cc_start: 0.7607 (tttt) cc_final: 0.7236 (tmmt) REVERT: D 243 ASN cc_start: 0.7878 (t0) cc_final: 0.7561 (t0) REVERT: D 244 TYR cc_start: 0.7982 (p90) cc_final: 0.7726 (p90) REVERT: D 440 LEU cc_start: 0.8751 (tp) cc_final: 0.8519 (tt) REVERT: E 18 LYS cc_start: 0.7905 (tttt) cc_final: 0.7265 (tmmt) REVERT: E 48 ASP cc_start: 0.7202 (m-30) cc_final: 0.6531 (m-30) REVERT: E 56 ASP cc_start: 0.8890 (p0) cc_final: 0.8655 (p0) REVERT: E 115 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7998 (tmm) REVERT: E 215 LYS cc_start: 0.8627 (tttt) cc_final: 0.8387 (tptp) REVERT: E 243 ASN cc_start: 0.7852 (t0) cc_final: 0.7479 (t0) REVERT: E 245 ASP cc_start: 0.7418 (p0) cc_final: 0.7167 (p0) REVERT: A 70 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8330 (mttp) REVERT: A 90 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: A 165 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: A 190 GLU cc_start: 0.8511 (tt0) cc_final: 0.8227 (tt0) outliers start: 49 outliers final: 31 residues processed: 359 average time/residue: 1.3206 time to fit residues: 532.0336 Evaluate side-chains 379 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 340 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain N residue 445 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 62 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 243 ASN C 265 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19240 Z= 0.262 Angle : 0.576 8.144 26155 Z= 0.305 Chirality : 0.046 0.155 2965 Planarity : 0.004 0.036 3235 Dihedral : 8.688 65.942 3170 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.13 % Allowed : 10.89 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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 (0.18), residues: 2240 helix: 1.49 (0.21), residues: 620 sheet: 0.61 (0.19), residues: 660 loop : 0.25 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.003 0.001 HIS E 119 PHE 0.018 0.002 PHE A 98 TYR 0.029 0.002 TYR E 299 ARG 0.005 0.001 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 344 time to evaluate : 2.168 Fit side-chains REVERT: B 18 LYS cc_start: 0.7639 (tttt) cc_final: 0.7118 (tmmt) REVERT: B 70 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8462 (mmtt) REVERT: K 447 TYR cc_start: 0.8427 (m-80) cc_final: 0.8109 (m-80) REVERT: O 468 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5657 (tp) REVERT: N 415 THR cc_start: 0.8006 (m) cc_final: 0.7718 (t) REVERT: C 18 LYS cc_start: 0.7695 (tttt) cc_final: 0.7259 (tmmt) REVERT: C 48 ASP cc_start: 0.7374 (m-30) cc_final: 0.6717 (m-30) REVERT: C 90 GLN cc_start: 0.8765 (mt0) cc_final: 0.8494 (mp10) REVERT: C 115 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8010 (tmm) REVERT: C 261 MET cc_start: 0.9065 (mmt) cc_final: 0.8616 (mmm) REVERT: D 18 LYS cc_start: 0.7601 (tttt) cc_final: 0.7228 (tmmt) REVERT: D 243 ASN cc_start: 0.7874 (t0) cc_final: 0.7550 (t0) REVERT: D 244 TYR cc_start: 0.7964 (p90) cc_final: 0.7702 (p90) REVERT: D 440 LEU cc_start: 0.8728 (tp) cc_final: 0.8515 (tt) REVERT: E 18 LYS cc_start: 0.7894 (tttt) cc_final: 0.7255 (tmmt) REVERT: E 48 ASP cc_start: 0.7173 (m-30) cc_final: 0.6491 (m-30) REVERT: E 56 ASP cc_start: 0.8884 (p0) cc_final: 0.8649 (p0) REVERT: E 115 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7968 (tmm) REVERT: E 215 LYS cc_start: 0.8625 (tttt) cc_final: 0.8386 (tptp) REVERT: E 243 ASN cc_start: 0.7822 (t0) cc_final: 0.7453 (t0) REVERT: A 70 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8328 (mttp) REVERT: A 90 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: A 165 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7550 (mm-30) REVERT: A 190 GLU cc_start: 0.8501 (tt0) cc_final: 0.8225 (tt0) outliers start: 42 outliers final: 32 residues processed: 357 average time/residue: 1.3571 time to fit residues: 542.9489 Evaluate side-chains 376 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 337 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain N residue 445 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 137 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 141 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 265 ASN C 243 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19240 Z= 0.263 Angle : 0.583 8.497 26155 Z= 0.308 Chirality : 0.046 0.154 2965 Planarity : 0.004 0.054 3235 Dihedral : 8.649 65.361 3170 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.28 % Allowed : 10.78 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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 (0.18), residues: 2240 helix: 1.48 (0.21), residues: 620 sheet: 0.61 (0.19), residues: 660 loop : 0.25 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.003 0.001 HIS E 119 PHE 0.018 0.002 PHE A 98 TYR 0.029 0.002 TYR E 299 ARG 0.006 0.001 ARG C 269 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 341 time to evaluate : 2.068 Fit side-chains REVERT: B 18 LYS cc_start: 0.7646 (tttt) cc_final: 0.7119 (tmmt) REVERT: B 70 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8462 (mmtt) REVERT: K 447 TYR cc_start: 0.8426 (m-80) cc_final: 0.8100 (m-80) REVERT: O 468 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5681 (tp) REVERT: N 415 THR cc_start: 0.8029 (m) cc_final: 0.7694 (t) REVERT: C 18 LYS cc_start: 0.7664 (tttt) cc_final: 0.7241 (tmmt) REVERT: C 48 ASP cc_start: 0.7375 (m-30) cc_final: 0.6712 (m-30) REVERT: C 90 GLN cc_start: 0.8764 (mt0) cc_final: 0.8492 (mp10) REVERT: C 115 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8007 (tmm) REVERT: C 261 MET cc_start: 0.9065 (mmt) cc_final: 0.8616 (mmm) REVERT: D 18 LYS cc_start: 0.7601 (tttt) cc_final: 0.7225 (tmmt) REVERT: D 49 MET cc_start: 0.7393 (tmm) cc_final: 0.7125 (pp-130) REVERT: D 243 ASN cc_start: 0.7871 (t0) cc_final: 0.7548 (t0) REVERT: D 244 TYR cc_start: 0.7941 (p90) cc_final: 0.7686 (p90) REVERT: D 440 LEU cc_start: 0.8728 (tp) cc_final: 0.8515 (tt) REVERT: E 18 LYS cc_start: 0.7901 (tttt) cc_final: 0.7253 (tmmt) REVERT: E 48 ASP cc_start: 0.7155 (m-30) cc_final: 0.6471 (m-30) REVERT: E 56 ASP cc_start: 0.8884 (p0) cc_final: 0.8640 (p0) REVERT: E 115 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7989 (tmm) REVERT: E 165 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: E 215 LYS cc_start: 0.8627 (tttt) cc_final: 0.8385 (tptp) REVERT: E 243 ASN cc_start: 0.7785 (t0) cc_final: 0.7477 (t0) REVERT: E 245 ASP cc_start: 0.7473 (p0) cc_final: 0.7174 (p0) REVERT: A 70 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8312 (mttp) REVERT: A 90 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8401 (mp10) REVERT: A 165 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: A 190 GLU cc_start: 0.8502 (tt0) cc_final: 0.8226 (tt0) outliers start: 45 outliers final: 34 residues processed: 357 average time/residue: 1.3156 time to fit residues: 526.1092 Evaluate side-chains 378 residues out of total 1975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 336 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain K residue 408 SER Chi-restraints excluded: chain O residue 468 LEU Chi-restraints excluded: chain O residue 497 THR Chi-restraints excluded: chain N residue 408 SER Chi-restraints excluded: chain N residue 445 THR Chi-restraints excluded: chain N residue 497 THR Chi-restraints excluded: chain M residue 408 SER Chi-restraints excluded: chain M residue 468 LEU Chi-restraints excluded: chain M residue 497 THR Chi-restraints excluded: chain L residue 408 SER Chi-restraints excluded: chain L residue 497 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 244 TYR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 90 GLN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 227 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 183 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 224 GLN B 265 ASN C 243 ASN E 185 GLN A 243 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.144577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108241 restraints weight = 17455.801| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.20 r_work: 0.2813 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19240 Z= 0.281 Angle : 0.595 8.482 26155 Z= 0.314 Chirality : 0.047 0.155 2965 Planarity : 0.004 0.077 3235 Dihedral : 8.701 65.696 3170 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.48 % Allowed : 10.48 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: 0.94 (0.18), residues: 2240 helix: 1.44 (0.21), residues: 620 sheet: 0.54 (0.19), residues: 685 loop : 0.29 (0.21), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.003 0.001 HIS D 107 PHE 0.018 0.002 PHE A 98 TYR 0.029 0.002 TYR E 299 ARG 0.010 0.001 ARG C 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8101.44 seconds wall clock time: 144 minutes 38.11 seconds (8678.11 seconds total)