Starting phenix.real_space_refine on Fri Sep 27 13:35:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hio_0226/09_2024/6hio_0226_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hio_0226/09_2024/6hio_0226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hio_0226/09_2024/6hio_0226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hio_0226/09_2024/6hio_0226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hio_0226/09_2024/6hio_0226_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hio_0226/09_2024/6hio_0226_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 45 5.16 5 C 10565 2.51 5 N 2585 2.21 5 O 2890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16085 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "E" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3134 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 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: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 1, 'SRO': 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: 9.87, per 1000 atoms: 0.61 Number of scatterers: 16085 At special positions: 0 Unit cell: (96.627, 94.549, 163.123, 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 45 16.00 O 2890 8.00 N 2585 7.00 C 10565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG B 501 " - " ASN B 82 " " NAG C 501 " - " ASN C 82 " " NAG D 902 " - " ASN D 82 " " NAG E 902 " - " ASN E 82 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN A 148 " " NAG H 1 " - " ASN E 164 " " NAG I 1 " - " ASN E 148 " " NAG J 1 " - " ASN B 164 " " NAG K 1 " - " ASN B 148 " " NAG L 1 " - " ASN C 164 " " NAG M 1 " - " ASN C 148 " " NAG N 1 " - " ASN D 164 " " NAG O 1 " - " ASN D 148 " Time building additional restraints: 4.12 Conformation dependent library (CDL) restraints added in 1.8 seconds 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 45.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.519A pdb=" N SER A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 240 removed outlier: 5.048A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 4.102A pdb=" N PHE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER A 248 " --> pdb=" O PRO A 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 248' Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.867A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.968A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 402 through 414 Processing helix chain 'A' and resid 415 through 460 removed outlier: 3.571A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.519A pdb=" N SER E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 240 removed outlier: 5.049A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix removed outlier: 4.102A pdb=" N PHE E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU E 234 " --> pdb=" O PRO E 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER E 248 " --> pdb=" O PRO E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 248' Processing helix chain 'E' and resid 249 through 273 removed outlier: 3.868A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR E 272 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.968A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET E 291 " --> pdb=" O PHE E 287 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA E 292 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 332 Processing helix chain 'E' and resid 402 through 414 Processing helix chain 'E' and resid 415 through 460 removed outlier: 3.571A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR E 431 " --> pdb=" O LEU E 427 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E 451 " --> pdb=" O ALA E 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 452 " --> pdb=" O TYR E 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.518A pdb=" N SER B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 240 removed outlier: 5.049A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix removed outlier: 4.101A pdb=" N PHE B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 234 " --> pdb=" O PRO B 230 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 236 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.582A pdb=" N SER B 248 " --> pdb=" O PRO B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 249 through 273 removed outlier: 3.867A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 272 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.968A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B 292 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 415 through 460 removed outlier: 3.571A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 53 through 56 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.519A pdb=" N SER C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 240 removed outlier: 5.050A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 4.101A pdb=" N PHE C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 236 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER C 248 " --> pdb=" O PRO C 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 248' Processing helix chain 'C' and resid 249 through 273 removed outlier: 3.867A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.969A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 332 Processing helix chain 'C' and resid 402 through 414 Processing helix chain 'C' and resid 415 through 460 removed outlier: 3.571A pdb=" N VAL C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR C 451 " --> pdb=" O ALA C 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 53 through 56 Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.519A pdb=" N SER D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 240 removed outlier: 5.049A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix removed outlier: 4.101A pdb=" N PHE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU D 234 " --> pdb=" O PRO D 230 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 236 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP D 238 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 248 removed outlier: 3.583A pdb=" N SER D 248 " --> pdb=" O PRO D 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 245 through 248' Processing helix chain 'D' and resid 249 through 273 removed outlier: 3.867A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR D 272 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.968A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA D 292 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 Processing helix chain 'D' and resid 402 through 414 Processing helix chain 'D' and resid 415 through 460 removed outlier: 3.572A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR D 431 " --> pdb=" O LEU D 427 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 105 removed outlier: 7.257A pdb=" N VAL A 132 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG A 65 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 89 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN A 195 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 103 through 105 removed outlier: 7.257A pdb=" N VAL E 132 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL E 57 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN E 50 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG E 65 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 89 Processing sheet with id=AA7, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 105 removed outlier: 7.256A pdb=" N VAL B 132 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 65 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP B 42 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 89 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.941A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.941A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN B 195 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 103 through 105 removed outlier: 7.257A pdb=" N VAL C 132 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG C 65 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 85 through 89 Processing sheet with id=AB6, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.942A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 195 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 105 removed outlier: 7.256A pdb=" N VAL D 132 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG D 65 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 85 through 89 Processing sheet with id=AC1, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.941A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.941A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN D 195 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.31 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4898 1.34 - 1.46: 4092 1.46 - 1.58: 7455 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 16515 Sorted by residual: bond pdb=" CG SRO D 901 " pdb=" CD2 SRO D 901 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CG SRO E 901 " pdb=" CD2 SRO E 901 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" CG SRO C 502 " pdb=" CD2 SRO C 502 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CG SRO B 502 " pdb=" CD2 SRO B 502 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CG SRO A 502 " pdb=" CD2 SRO A 502 " ideal model delta sigma weight residual 1.438 1.350 0.088 2.00e-02 2.50e+03 1.91e+01 ... (remaining 16510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 22367 4.32 - 8.64: 178 8.64 - 12.96: 15 12.96 - 17.28: 5 17.28 - 21.60: 5 Bond angle restraints: 22570 Sorted by residual: angle pdb=" CA LEU B 131 " pdb=" CB LEU B 131 " pdb=" CG LEU B 131 " ideal model delta sigma weight residual 116.30 137.90 -21.60 3.50e+00 8.16e-02 3.81e+01 angle pdb=" CA LEU C 131 " pdb=" CB LEU C 131 " pdb=" CG LEU C 131 " ideal model delta sigma weight residual 116.30 137.90 -21.60 3.50e+00 8.16e-02 3.81e+01 angle pdb=" CA LEU D 131 " pdb=" CB LEU D 131 " pdb=" CG LEU D 131 " ideal model delta sigma weight residual 116.30 137.90 -21.60 3.50e+00 8.16e-02 3.81e+01 angle pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " pdb=" CG LEU A 131 " ideal model delta sigma weight residual 116.30 137.87 -21.57 3.50e+00 8.16e-02 3.80e+01 angle pdb=" CA LEU E 131 " pdb=" CB LEU E 131 " pdb=" CG LEU E 131 " ideal model delta sigma weight residual 116.30 137.81 -21.51 3.50e+00 8.16e-02 3.78e+01 ... (remaining 22565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 9291 15.87 - 31.74: 539 31.74 - 47.60: 160 47.60 - 63.47: 30 63.47 - 79.34: 25 Dihedral angle restraints: 10045 sinusoidal: 4305 harmonic: 5740 Sorted by residual: dihedral pdb=" CA GLN D 66 " pdb=" C GLN D 66 " pdb=" N TYR D 67 " pdb=" CA TYR D 67 " ideal model delta harmonic sigma weight residual 180.00 146.64 33.36 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA GLN A 66 " pdb=" C GLN A 66 " pdb=" N TYR A 67 " pdb=" CA TYR A 67 " ideal model delta harmonic sigma weight residual 180.00 146.65 33.35 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA GLN C 66 " pdb=" C GLN C 66 " pdb=" N TYR C 67 " pdb=" CA TYR C 67 " ideal model delta harmonic sigma weight residual 180.00 146.65 33.35 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 10042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1755 0.053 - 0.106: 714 0.106 - 0.160: 151 0.160 - 0.213: 45 0.213 - 0.266: 15 Chirality restraints: 2680 Sorted by residual: chirality pdb=" CG LEU A 131 " pdb=" CB LEU A 131 " pdb=" CD1 LEU A 131 " pdb=" CD2 LEU A 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU E 131 " pdb=" CB LEU E 131 " pdb=" CD1 LEU E 131 " pdb=" CD2 LEU E 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU C 131 " pdb=" CB LEU C 131 " pdb=" CD1 LEU C 131 " pdb=" CD2 LEU C 131 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 2677 not shown) Planarity restraints: 2765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 168 " -0.016 2.00e-02 2.50e+03 1.81e-02 8.23e+00 pdb=" CG TRP C 168 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 168 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 168 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 168 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 168 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 168 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 168 " -0.016 2.00e-02 2.50e+03 1.80e-02 8.12e+00 pdb=" CG TRP D 168 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 168 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP D 168 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 168 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP D 168 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 168 " -0.016 2.00e-02 2.50e+03 1.80e-02 8.10e+00 pdb=" CG TRP B 168 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 168 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 168 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 168 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 168 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 168 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 168 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 168 " 0.002 2.00e-02 2.50e+03 ... (remaining 2762 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1414 2.73 - 3.27: 16077 3.27 - 3.81: 27559 3.81 - 4.36: 31212 4.36 - 4.90: 51884 Nonbonded interactions: 128146 Sorted by model distance: nonbonded pdb=" OD2 ASP C 238 " pdb=" CD1 LEU C 294 " model vdw 2.185 3.460 nonbonded pdb=" OD2 ASP A 238 " pdb=" CD1 LEU A 294 " model vdw 2.185 3.460 nonbonded pdb=" OD2 ASP B 238 " pdb=" CD1 LEU B 294 " model vdw 2.186 3.460 nonbonded pdb=" OD2 ASP E 238 " pdb=" CD1 LEU E 294 " model vdw 2.186 3.460 nonbonded pdb=" OD2 ASP D 238 " pdb=" CD1 LEU D 294 " model vdw 2.186 3.460 ... (remaining 128141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 460) selection = (chain 'B' and resid 9 through 460) selection = (chain 'C' and resid 9 through 460) selection = (chain 'D' and resid 9 through 460) selection = (chain 'E' and resid 9 through 460) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.010 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.080 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.010 0.088 16515 Z= 0.614 Angle : 1.172 21.599 22570 Z= 0.574 Chirality : 0.062 0.266 2680 Planarity : 0.006 0.058 2750 Dihedral : 12.199 79.339 6290 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.29 % Allowed : 10.14 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.16), residues: 1905 helix: -2.64 (0.14), residues: 640 sheet: -2.24 (0.25), residues: 340 loop : -2.49 (0.18), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP C 168 HIS 0.009 0.003 HIS B 309 PHE 0.025 0.004 PHE E 153 TYR 0.030 0.003 TYR A 116 ARG 0.005 0.001 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7853 (p0) cc_final: 0.7643 (p0) REVERT: A 254 PHE cc_start: 0.9440 (t80) cc_final: 0.9229 (t80) REVERT: A 441 TYR cc_start: 0.8368 (t80) cc_final: 0.8040 (t80) REVERT: E 210 MET cc_start: 0.7966 (tmm) cc_final: 0.7764 (tmm) REVERT: E 254 PHE cc_start: 0.9462 (t80) cc_final: 0.9140 (t80) REVERT: E 259 LEU cc_start: 0.9583 (mm) cc_final: 0.9340 (mm) REVERT: E 441 TYR cc_start: 0.8453 (t80) cc_final: 0.8111 (t80) REVERT: B 254 PHE cc_start: 0.9518 (t80) cc_final: 0.9279 (t80) REVERT: B 259 LEU cc_start: 0.9560 (mm) cc_final: 0.9354 (mm) REVERT: B 441 TYR cc_start: 0.8453 (t80) cc_final: 0.8076 (t80) REVERT: C 254 PHE cc_start: 0.9519 (t80) cc_final: 0.9163 (t80) REVERT: C 259 LEU cc_start: 0.9591 (mm) cc_final: 0.9312 (mm) REVERT: D 52 ASP cc_start: 0.7942 (p0) cc_final: 0.7715 (p0) REVERT: D 254 PHE cc_start: 0.9479 (t80) cc_final: 0.9252 (t80) REVERT: D 259 LEU cc_start: 0.9611 (mm) cc_final: 0.9339 (mm) outliers start: 5 outliers final: 5 residues processed: 154 average time/residue: 0.2785 time to fit residues: 64.7662 Evaluate side-chains 103 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 7.9990 chunk 144 optimal weight: 0.3980 chunk 79 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.0270 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 overall best weight: 0.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 119 HIS A 124 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 GLN E 101 ASN E 119 HIS E 124 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN B 119 HIS B 124 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 158 HIS B 311 GLN C 119 HIS C 124 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 158 HIS D 119 HIS ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16515 Z= 0.212 Angle : 0.729 7.439 22570 Z= 0.370 Chirality : 0.047 0.233 2680 Planarity : 0.005 0.039 2750 Dihedral : 9.910 84.116 2645 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.12 % Allowed : 3.13 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.17), residues: 1905 helix: -1.38 (0.16), residues: 760 sheet: -2.43 (0.23), residues: 400 loop : -2.08 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 168 HIS 0.002 0.001 HIS B 309 PHE 0.014 0.002 PHE D 212 TYR 0.022 0.002 TYR B 67 ARG 0.005 0.001 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8448 (m-40) cc_final: 0.7959 (p0) REVERT: A 210 MET cc_start: 0.8017 (tmm) cc_final: 0.7779 (tmm) REVERT: A 235 MET cc_start: 0.8817 (mmt) cc_final: 0.8278 (mmt) REVERT: A 254 PHE cc_start: 0.9450 (t80) cc_final: 0.9123 (t80) REVERT: A 441 TYR cc_start: 0.8137 (t80) cc_final: 0.7845 (t80) REVERT: E 259 LEU cc_start: 0.9422 (mm) cc_final: 0.9213 (mm) REVERT: E 403 LEU cc_start: 0.9292 (tp) cc_final: 0.9087 (pt) REVERT: E 419 MET cc_start: 0.9355 (ptp) cc_final: 0.9055 (ptm) REVERT: B 254 PHE cc_start: 0.9547 (t80) cc_final: 0.9107 (t80) REVERT: B 258 LEU cc_start: 0.9734 (mm) cc_final: 0.9413 (mm) REVERT: B 419 MET cc_start: 0.9358 (ptp) cc_final: 0.9043 (ptm) REVERT: B 436 LEU cc_start: 0.9242 (mm) cc_final: 0.9021 (pp) REVERT: C 254 PHE cc_start: 0.9563 (t80) cc_final: 0.9304 (t80) REVERT: C 259 LEU cc_start: 0.9484 (mm) cc_final: 0.9089 (mm) REVERT: C 419 MET cc_start: 0.9192 (ptp) cc_final: 0.8736 (ptm) REVERT: D 210 MET cc_start: 0.8075 (tmm) cc_final: 0.7820 (tmm) REVERT: D 254 PHE cc_start: 0.9553 (t80) cc_final: 0.9141 (t80) REVERT: D 419 MET cc_start: 0.9398 (ptp) cc_final: 0.9027 (ptm) outliers start: 2 outliers final: 1 residues processed: 149 average time/residue: 0.2329 time to fit residues: 55.8398 Evaluate side-chains 106 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 HIS ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 HIS ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16515 Z= 0.383 Angle : 0.734 8.117 22570 Z= 0.369 Chirality : 0.045 0.172 2680 Planarity : 0.004 0.038 2750 Dihedral : 8.725 74.801 2645 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.18), residues: 1905 helix: -0.49 (0.17), residues: 770 sheet: -2.52 (0.22), residues: 395 loop : -1.80 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 168 HIS 0.004 0.001 HIS C 158 PHE 0.023 0.002 PHE E 265 TYR 0.024 0.002 TYR A 67 ARG 0.005 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8654 (m-40) cc_final: 0.8203 (p0) REVERT: A 210 MET cc_start: 0.8160 (tmm) cc_final: 0.7911 (tmm) REVERT: A 235 MET cc_start: 0.8682 (mmt) cc_final: 0.8436 (mmt) REVERT: A 441 TYR cc_start: 0.8064 (t80) cc_final: 0.7827 (t80) REVERT: E 403 LEU cc_start: 0.9356 (tp) cc_final: 0.9139 (pt) REVERT: E 419 MET cc_start: 0.9464 (ptp) cc_final: 0.9152 (ptm) REVERT: E 441 TYR cc_start: 0.8330 (t80) cc_final: 0.7982 (t80) REVERT: B 238 ASP cc_start: 0.8040 (t70) cc_final: 0.7804 (t0) REVERT: B 254 PHE cc_start: 0.9567 (t80) cc_final: 0.9208 (t80) REVERT: B 258 LEU cc_start: 0.9712 (mm) cc_final: 0.9499 (mm) REVERT: B 419 MET cc_start: 0.9433 (ptp) cc_final: 0.9091 (ptm) REVERT: B 441 TYR cc_start: 0.8016 (t80) cc_final: 0.7716 (t80) REVERT: C 210 MET cc_start: 0.9040 (tpp) cc_final: 0.8745 (tpp) REVERT: C 419 MET cc_start: 0.9403 (ptp) cc_final: 0.8987 (ptm) REVERT: C 436 LEU cc_start: 0.9296 (mm) cc_final: 0.9090 (pp) REVERT: D 52 ASP cc_start: 0.8042 (p0) cc_final: 0.7809 (p0) REVERT: D 210 MET cc_start: 0.8187 (tmm) cc_final: 0.7944 (tmm) REVERT: D 254 PHE cc_start: 0.9497 (t80) cc_final: 0.9199 (t80) REVERT: D 258 LEU cc_start: 0.9738 (mm) cc_final: 0.9497 (mm) REVERT: D 419 MET cc_start: 0.9549 (ptp) cc_final: 0.9198 (ptm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2568 time to fit residues: 47.0963 Evaluate side-chains 93 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16515 Z= 0.192 Angle : 0.634 6.303 22570 Z= 0.319 Chirality : 0.045 0.198 2680 Planarity : 0.004 0.031 2750 Dihedral : 7.989 75.336 2645 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 1905 helix: -0.02 (0.18), residues: 770 sheet: -2.45 (0.23), residues: 385 loop : -1.72 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 156 HIS 0.002 0.000 HIS E 18 PHE 0.013 0.001 PHE B 254 TYR 0.022 0.002 TYR A 67 ARG 0.002 0.000 ARG E 420 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8550 (m-40) cc_final: 0.8081 (p0) REVERT: A 238 ASP cc_start: 0.7921 (t70) cc_final: 0.7687 (t0) REVERT: A 441 TYR cc_start: 0.7941 (t80) cc_final: 0.7698 (t80) REVERT: E 235 MET cc_start: 0.8489 (mmt) cc_final: 0.8242 (mpp) REVERT: E 419 MET cc_start: 0.9450 (ptp) cc_final: 0.9101 (ptm) REVERT: B 254 PHE cc_start: 0.9564 (t80) cc_final: 0.9297 (t80) REVERT: B 258 LEU cc_start: 0.9678 (mm) cc_final: 0.9437 (mm) REVERT: B 419 MET cc_start: 0.9424 (ptp) cc_final: 0.9067 (ptm) REVERT: B 441 TYR cc_start: 0.7927 (t80) cc_final: 0.7674 (t80) REVERT: C 210 MET cc_start: 0.8921 (tpp) cc_final: 0.8643 (tpp) REVERT: C 232 ILE cc_start: 0.9510 (pt) cc_final: 0.9259 (tt) REVERT: C 235 MET cc_start: 0.8594 (mmt) cc_final: 0.7920 (mpp) REVERT: C 254 PHE cc_start: 0.9596 (t80) cc_final: 0.9319 (t80) REVERT: C 419 MET cc_start: 0.9412 (ptp) cc_final: 0.9035 (ptm) REVERT: C 436 LEU cc_start: 0.9303 (mm) cc_final: 0.9098 (pp) REVERT: D 235 MET cc_start: 0.8773 (mmt) cc_final: 0.8392 (mpp) REVERT: D 254 PHE cc_start: 0.9505 (t80) cc_final: 0.9151 (t80) REVERT: D 258 LEU cc_start: 0.9700 (mm) cc_final: 0.9390 (mm) REVERT: D 419 MET cc_start: 0.9527 (ptp) cc_final: 0.9183 (ptm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2226 time to fit residues: 42.7069 Evaluate side-chains 94 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 156 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16515 Z= 0.177 Angle : 0.609 6.408 22570 Z= 0.305 Chirality : 0.044 0.167 2680 Planarity : 0.004 0.031 2750 Dihedral : 7.028 70.405 2645 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.19), residues: 1905 helix: 0.39 (0.18), residues: 775 sheet: -2.53 (0.22), residues: 400 loop : -1.43 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 168 HIS 0.002 0.000 HIS E 18 PHE 0.025 0.001 PHE E 254 TYR 0.015 0.001 TYR A 67 ARG 0.002 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8529 (m-40) cc_final: 0.8064 (p0) REVERT: A 419 MET cc_start: 0.9464 (ptp) cc_final: 0.9185 (ptp) REVERT: E 235 MET cc_start: 0.8562 (mmt) cc_final: 0.8337 (mpp) REVERT: E 419 MET cc_start: 0.9450 (ptp) cc_final: 0.9093 (ptm) REVERT: B 210 MET cc_start: 0.8991 (tpp) cc_final: 0.8686 (tpp) REVERT: B 235 MET cc_start: 0.8742 (mpp) cc_final: 0.8424 (mpp) REVERT: B 254 PHE cc_start: 0.9510 (t80) cc_final: 0.9263 (t80) REVERT: B 258 LEU cc_start: 0.9659 (mm) cc_final: 0.9356 (mm) REVERT: B 419 MET cc_start: 0.9391 (ptp) cc_final: 0.9064 (ptm) REVERT: C 210 MET cc_start: 0.8902 (tpp) cc_final: 0.8614 (tpp) REVERT: C 235 MET cc_start: 0.8586 (mmt) cc_final: 0.8070 (mmt) REVERT: C 419 MET cc_start: 0.9445 (ptp) cc_final: 0.8978 (ppp) REVERT: C 436 LEU cc_start: 0.9300 (mm) cc_final: 0.9084 (pp) REVERT: C 441 TYR cc_start: 0.8290 (t80) cc_final: 0.8048 (t80) REVERT: D 235 MET cc_start: 0.8762 (mmt) cc_final: 0.8550 (mmt) REVERT: D 254 PHE cc_start: 0.9498 (t80) cc_final: 0.9193 (t80) REVERT: D 258 LEU cc_start: 0.9716 (mm) cc_final: 0.9452 (mm) REVERT: D 419 MET cc_start: 0.9507 (ptp) cc_final: 0.9185 (ptm) REVERT: D 436 LEU cc_start: 0.9220 (mm) cc_final: 0.8998 (pp) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2463 time to fit residues: 46.5224 Evaluate side-chains 97 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16515 Z= 0.275 Angle : 0.646 8.037 22570 Z= 0.320 Chirality : 0.044 0.167 2680 Planarity : 0.004 0.033 2750 Dihedral : 6.731 66.577 2645 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.19), residues: 1905 helix: 0.62 (0.18), residues: 775 sheet: -2.46 (0.23), residues: 380 loop : -1.46 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 168 HIS 0.002 0.001 HIS E 18 PHE 0.021 0.002 PHE B 242 TYR 0.022 0.001 TYR B 441 ARG 0.002 0.000 ARG C 420 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8595 (m-40) cc_final: 0.8172 (p0) REVERT: A 403 LEU cc_start: 0.9481 (tp) cc_final: 0.9269 (pt) REVERT: A 419 MET cc_start: 0.9470 (ptp) cc_final: 0.9173 (ptp) REVERT: E 235 MET cc_start: 0.8571 (mmt) cc_final: 0.8326 (mpp) REVERT: E 419 MET cc_start: 0.9453 (ptp) cc_final: 0.9090 (ptm) REVERT: B 210 MET cc_start: 0.9029 (tpp) cc_final: 0.8687 (tpp) REVERT: B 235 MET cc_start: 0.8729 (mpp) cc_final: 0.8412 (mpp) REVERT: B 419 MET cc_start: 0.9410 (ptp) cc_final: 0.9103 (ptm) REVERT: C 210 MET cc_start: 0.8929 (tpp) cc_final: 0.8620 (tpp) REVERT: C 235 MET cc_start: 0.8633 (mmt) cc_final: 0.7974 (mpp) REVERT: C 419 MET cc_start: 0.9463 (ptp) cc_final: 0.9091 (ptm) REVERT: D 254 PHE cc_start: 0.9470 (t80) cc_final: 0.9184 (t80) REVERT: D 258 LEU cc_start: 0.9643 (mm) cc_final: 0.9342 (mm) REVERT: D 419 MET cc_start: 0.9521 (ptp) cc_final: 0.9221 (ptm) REVERT: D 436 LEU cc_start: 0.9231 (mm) cc_final: 0.9016 (pp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2370 time to fit residues: 42.5727 Evaluate side-chains 93 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 124 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16515 Z= 0.270 Angle : 0.659 7.531 22570 Z= 0.324 Chirality : 0.044 0.164 2680 Planarity : 0.004 0.036 2750 Dihedral : 6.546 62.746 2645 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.20), residues: 1905 helix: 0.90 (0.19), residues: 775 sheet: -2.53 (0.22), residues: 390 loop : -1.23 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 168 HIS 0.002 0.001 HIS D 158 PHE 0.026 0.002 PHE E 254 TYR 0.023 0.001 TYR B 441 ARG 0.001 0.000 ARG E 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8566 (m-40) cc_final: 0.8177 (p0) REVERT: A 419 MET cc_start: 0.9460 (ptp) cc_final: 0.9112 (ptp) REVERT: E 235 MET cc_start: 0.8548 (mmt) cc_final: 0.8250 (mpp) REVERT: E 419 MET cc_start: 0.9462 (ptp) cc_final: 0.9105 (ptm) REVERT: B 210 MET cc_start: 0.9044 (tpp) cc_final: 0.8696 (tpp) REVERT: B 235 MET cc_start: 0.8722 (mpp) cc_final: 0.8446 (mpp) REVERT: B 258 LEU cc_start: 0.9616 (mm) cc_final: 0.9389 (mm) REVERT: B 419 MET cc_start: 0.9403 (ptp) cc_final: 0.9080 (ptm) REVERT: C 210 MET cc_start: 0.8939 (tpp) cc_final: 0.8614 (tpp) REVERT: C 235 MET cc_start: 0.8632 (mmt) cc_final: 0.8081 (mpp) REVERT: C 419 MET cc_start: 0.9459 (ptp) cc_final: 0.9079 (ptm) REVERT: D 254 PHE cc_start: 0.9459 (t80) cc_final: 0.9169 (t80) REVERT: D 258 LEU cc_start: 0.9655 (mm) cc_final: 0.9369 (mm) REVERT: D 419 MET cc_start: 0.9479 (ptp) cc_final: 0.9180 (ptm) REVERT: D 436 LEU cc_start: 0.9255 (mm) cc_final: 0.9042 (pp) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.2514 time to fit residues: 44.7838 Evaluate side-chains 98 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 116 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 0.0050 chunk 143 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16515 Z= 0.166 Angle : 0.625 7.820 22570 Z= 0.304 Chirality : 0.044 0.193 2680 Planarity : 0.004 0.036 2750 Dihedral : 6.353 62.129 2645 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1905 helix: 0.99 (0.19), residues: 775 sheet: -2.59 (0.22), residues: 415 loop : -0.97 (0.26), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 156 HIS 0.001 0.000 HIS C 118 PHE 0.025 0.001 PHE B 242 TYR 0.035 0.002 TYR B 441 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8530 (m-40) cc_final: 0.8155 (p0) REVERT: A 419 MET cc_start: 0.9438 (ptp) cc_final: 0.9154 (ptp) REVERT: E 235 MET cc_start: 0.8562 (mmt) cc_final: 0.8235 (mpp) REVERT: E 419 MET cc_start: 0.9442 (ptp) cc_final: 0.9096 (ptm) REVERT: E 436 LEU cc_start: 0.9232 (mm) cc_final: 0.9003 (pp) REVERT: B 210 MET cc_start: 0.9083 (tpp) cc_final: 0.8690 (tpp) REVERT: B 235 MET cc_start: 0.8720 (mpp) cc_final: 0.8398 (mpp) REVERT: B 254 PHE cc_start: 0.9365 (t80) cc_final: 0.9139 (t80) REVERT: B 258 LEU cc_start: 0.9625 (mm) cc_final: 0.9388 (mm) REVERT: B 419 MET cc_start: 0.9362 (ptp) cc_final: 0.9031 (ptm) REVERT: C 210 MET cc_start: 0.8948 (tpp) cc_final: 0.8621 (tpp) REVERT: C 235 MET cc_start: 0.8655 (mmt) cc_final: 0.8079 (mpp) REVERT: C 419 MET cc_start: 0.9444 (ptp) cc_final: 0.8981 (ppp) REVERT: C 436 LEU cc_start: 0.9271 (mm) cc_final: 0.9062 (pp) REVERT: D 223 TYR cc_start: 0.8841 (m-10) cc_final: 0.8377 (m-10) REVERT: D 235 MET cc_start: 0.8709 (mmt) cc_final: 0.8382 (mpp) REVERT: D 254 PHE cc_start: 0.9458 (t80) cc_final: 0.9148 (t80) REVERT: D 258 LEU cc_start: 0.9639 (mm) cc_final: 0.9323 (mm) REVERT: D 419 MET cc_start: 0.9453 (ptp) cc_final: 0.9154 (ptm) REVERT: D 436 LEU cc_start: 0.9235 (mm) cc_final: 0.9023 (pp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2443 time to fit residues: 44.7007 Evaluate side-chains 100 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 chunk 175 optimal weight: 0.0980 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 112 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16515 Z= 0.188 Angle : 0.621 7.650 22570 Z= 0.301 Chirality : 0.044 0.170 2680 Planarity : 0.004 0.036 2750 Dihedral : 6.137 60.257 2645 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.06 % Allowed : 0.64 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1905 helix: 1.10 (0.19), residues: 775 sheet: -2.55 (0.22), residues: 415 loop : -0.92 (0.26), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 156 HIS 0.001 0.000 HIS C 158 PHE 0.028 0.001 PHE B 242 TYR 0.013 0.001 TYR B 441 ARG 0.002 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8548 (m-40) cc_final: 0.8160 (p0) REVERT: A 419 MET cc_start: 0.9453 (ptp) cc_final: 0.9183 (ptp) REVERT: E 235 MET cc_start: 0.8550 (mmt) cc_final: 0.8274 (mpp) REVERT: E 419 MET cc_start: 0.9452 (ptp) cc_final: 0.9126 (ptm) REVERT: E 436 LEU cc_start: 0.9219 (mm) cc_final: 0.8999 (pp) REVERT: B 210 MET cc_start: 0.9081 (tpp) cc_final: 0.8718 (tpp) REVERT: B 235 MET cc_start: 0.8684 (mpp) cc_final: 0.8406 (mpp) REVERT: B 258 LEU cc_start: 0.9646 (mm) cc_final: 0.9443 (mm) REVERT: B 419 MET cc_start: 0.9396 (ptp) cc_final: 0.9101 (ptm) REVERT: B 436 LEU cc_start: 0.9251 (mm) cc_final: 0.9045 (pp) REVERT: C 210 MET cc_start: 0.8938 (tpp) cc_final: 0.8609 (tpp) REVERT: C 235 MET cc_start: 0.8605 (mmt) cc_final: 0.8144 (mmt) REVERT: C 419 MET cc_start: 0.9429 (ptp) cc_final: 0.8959 (ppp) REVERT: C 436 LEU cc_start: 0.9315 (mm) cc_final: 0.9084 (pp) REVERT: D 223 TYR cc_start: 0.8856 (m-10) cc_final: 0.8461 (m-80) REVERT: D 235 MET cc_start: 0.8729 (mmt) cc_final: 0.8474 (mpp) REVERT: D 254 PHE cc_start: 0.9480 (t80) cc_final: 0.9133 (t80) REVERT: D 258 LEU cc_start: 0.9680 (mm) cc_final: 0.9341 (mm) REVERT: D 419 MET cc_start: 0.9441 (ptp) cc_final: 0.9152 (ptm) REVERT: D 436 LEU cc_start: 0.9222 (mm) cc_final: 0.9017 (pp) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.2304 time to fit residues: 41.8532 Evaluate side-chains 97 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16515 Z= 0.149 Angle : 0.617 8.392 22570 Z= 0.298 Chirality : 0.044 0.241 2680 Planarity : 0.003 0.035 2750 Dihedral : 6.029 61.245 2645 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.12 % Allowed : 0.35 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.20), residues: 1905 helix: 1.08 (0.19), residues: 780 sheet: -2.39 (0.23), residues: 405 loop : -1.01 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 156 HIS 0.001 0.000 HIS D 158 PHE 0.028 0.001 PHE E 254 TYR 0.014 0.001 TYR C 67 ARG 0.003 0.000 ARG E 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3810 Ramachandran restraints generated. 1905 Oldfield, 0 Emsley, 1905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8517 (m-40) cc_final: 0.8131 (p0) REVERT: A 210 MET cc_start: 0.9014 (tpp) cc_final: 0.8772 (tpp) REVERT: A 419 MET cc_start: 0.9427 (ptp) cc_final: 0.9175 (ptp) REVERT: E 210 MET cc_start: 0.9063 (mmm) cc_final: 0.8723 (tpp) REVERT: E 235 MET cc_start: 0.8509 (mmt) cc_final: 0.8263 (mpp) REVERT: E 436 LEU cc_start: 0.9186 (mm) cc_final: 0.8981 (pp) REVERT: B 210 MET cc_start: 0.9058 (tpp) cc_final: 0.8669 (tpp) REVERT: B 235 MET cc_start: 0.8663 (mpp) cc_final: 0.8424 (mpp) REVERT: B 419 MET cc_start: 0.9365 (ptp) cc_final: 0.9084 (ptm) REVERT: B 436 LEU cc_start: 0.9251 (mm) cc_final: 0.9038 (pp) REVERT: C 210 MET cc_start: 0.8930 (tpp) cc_final: 0.8605 (tpp) REVERT: C 235 MET cc_start: 0.8603 (mmt) cc_final: 0.8155 (mmt) REVERT: C 419 MET cc_start: 0.9403 (ptp) cc_final: 0.8949 (ppp) REVERT: C 436 LEU cc_start: 0.9307 (mm) cc_final: 0.9055 (pp) REVERT: D 223 TYR cc_start: 0.8887 (m-10) cc_final: 0.8496 (m-80) REVERT: D 254 PHE cc_start: 0.9408 (t80) cc_final: 0.9147 (t80) REVERT: D 258 LEU cc_start: 0.9690 (mm) cc_final: 0.9465 (mm) outliers start: 2 outliers final: 0 residues processed: 124 average time/residue: 0.2292 time to fit residues: 46.5840 Evaluate side-chains 103 residues out of total 1795 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 chunk 22 optimal weight: 0.0040 chunk 41 optimal weight: 0.4980 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.069995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.053144 restraints weight = 68285.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054731 restraints weight = 35043.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.055747 restraints weight = 21941.167| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16515 Z= 0.165 Angle : 0.613 7.872 22570 Z= 0.296 Chirality : 0.044 0.181 2680 Planarity : 0.003 0.035 2750 Dihedral : 5.883 59.460 2645 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.17 % Allowed : 0.29 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.20), residues: 1905 helix: 1.12 (0.19), residues: 800 sheet: -2.35 (0.23), residues: 405 loop : -0.96 (0.26), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 156 HIS 0.001 0.000 HIS A 158 PHE 0.028 0.001 PHE C 254 TYR 0.021 0.001 TYR E 223 ARG 0.002 0.000 ARG D 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.78 seconds wall clock time: 44 minutes 50.30 seconds (2690.30 seconds total)