Starting phenix.real_space_refine on Fri Feb 16 22:20:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsp_29421/02_2024/8fsp_29421_neut_updated.pdb" } resolution = 3.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 10985 2.51 5 N 2710 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16685 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "C" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {'NAG': 3, 'Y82': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.88, per 1000 atoms: 0.53 Number of scatterers: 16685 At special positions: 0 Unit cell: (103.4, 101.2, 169.4, 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 2945 8.00 N 2710 7.00 C 10985 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 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 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG A 502 " - " ASN A 148 " " NAG A 503 " - " ASN A 164 " " NAG B 501 " - " ASN B 82 " " NAG B 502 " - " ASN B 148 " " NAG B 503 " - " ASN B 164 " " NAG C 501 " - " ASN C 82 " " NAG C 502 " - " ASN C 148 " " NAG C 503 " - " ASN C 164 " " NAG D 501 " - " ASN D 82 " " NAG D 502 " - " ASN D 148 " " NAG D 503 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 6.94 Conformation dependent library (CDL) restraints added in 3.0 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 15 sheets defined 41.8% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'A' and resid 11 through 20 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 222 through 234 removed outlier: 4.048A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 237 through 240 No H-bonds generated for 'chain 'A' and resid 237 through 240' Processing helix chain 'A' and resid 248 through 272 removed outlier: 3.975A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 309 removed outlier: 3.835A pdb=" N VAL A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 398 through 431 removed outlier: 3.541A pdb=" N SER A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 464 removed outlier: 3.745A pdb=" N ASN A 464 " --> pdb=" O HIS A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 222 through 234 removed outlier: 4.049A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 237 through 240 No H-bonds generated for 'chain 'B' and resid 237 through 240' Processing helix chain 'B' and resid 248 through 272 removed outlier: 3.974A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 269 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 309 removed outlier: 3.835A pdb=" N VAL B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 398 through 431 removed outlier: 3.540A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 464 removed outlier: 3.745A pdb=" N ASN B 464 " --> pdb=" O HIS B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 222 through 234 removed outlier: 4.048A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 237 through 240 No H-bonds generated for 'chain 'C' and resid 237 through 240' Processing helix chain 'C' and resid 248 through 272 removed outlier: 3.975A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 269 " --> pdb=" O PHE C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 309 removed outlier: 3.836A pdb=" N VAL C 305 " --> pdb=" O THR C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 398 through 431 removed outlier: 3.540A pdb=" N SER C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS C 411 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP C 417 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 464 removed outlier: 3.745A pdb=" N ASN C 464 " --> pdb=" O HIS C 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 222 through 234 removed outlier: 4.048A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 237 through 240 No H-bonds generated for 'chain 'D' and resid 237 through 240' Processing helix chain 'D' and resid 248 through 272 removed outlier: 3.974A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL D 269 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 309 removed outlier: 3.835A pdb=" N VAL D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 398 through 431 removed outlier: 3.540A pdb=" N SER D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS D 411 " --> pdb=" O SER D 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP D 417 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 464 removed outlier: 3.745A pdb=" N ASN D 464 " --> pdb=" O HIS D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 222 through 234 removed outlier: 4.048A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 237 through 240 No H-bonds generated for 'chain 'E' and resid 237 through 240' Processing helix chain 'E' and resid 248 through 272 removed outlier: 3.974A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 269 " --> pdb=" O PHE E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 309 removed outlier: 3.836A pdb=" N VAL E 305 " --> pdb=" O THR E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'E' and resid 398 through 431 removed outlier: 3.540A pdb=" N SER E 407 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS E 411 " --> pdb=" O SER E 407 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ARG E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 464 removed outlier: 3.744A pdb=" N ASN E 464 " --> pdb=" O HIS E 460 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 163 through 167 removed outlier: 7.055A pdb=" N THR A 37 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N THR A 166 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 39 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.684A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 52 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 57 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 removed outlier: 5.102A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 209 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 197 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 163 through 167 removed outlier: 7.054A pdb=" N THR B 37 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N THR B 166 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL B 39 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.684A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 52 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 57 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 100 removed outlier: 5.102A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU B 209 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS B 197 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 163 through 167 removed outlier: 7.055A pdb=" N THR C 37 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N THR C 166 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 39 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.684A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C 52 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 57 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 98 through 100 removed outlier: 5.102A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 209 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 197 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 163 through 167 removed outlier: 7.055A pdb=" N THR D 37 " --> pdb=" O ASN D 164 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N THR D 166 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 39 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.684A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP D 52 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 57 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 98 through 100 removed outlier: 5.102A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU D 209 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 197 " --> pdb=" O GLU D 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 163 through 167 removed outlier: 7.055A pdb=" N THR E 37 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N THR E 166 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL E 39 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.685A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP E 52 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 57 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 98 through 100 removed outlier: 5.103A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU E 209 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E 197 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2115 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: 4.71 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2580 1.32 - 1.44: 4915 1.44 - 1.57: 9590 1.57 - 1.69: 0 1.69 - 1.82: 70 Bond restraints: 17155 Sorted by residual: bond pdb=" C7 Y82 C 504 " pdb=" C9 Y82 C 504 " ideal model delta sigma weight residual 1.894 1.470 0.424 2.00e-02 2.50e+03 4.49e+02 bond pdb=" C7 Y82 A 504 " pdb=" C9 Y82 A 504 " ideal model delta sigma weight residual 1.894 1.471 0.423 2.00e-02 2.50e+03 4.48e+02 bond pdb=" C7 Y82 E 501 " pdb=" C9 Y82 E 501 " ideal model delta sigma weight residual 1.894 1.471 0.423 2.00e-02 2.50e+03 4.47e+02 bond pdb=" C7 Y82 B 504 " pdb=" C9 Y82 B 504 " ideal model delta sigma weight residual 1.894 1.471 0.423 2.00e-02 2.50e+03 4.47e+02 bond pdb=" C7 Y82 D 504 " pdb=" C9 Y82 D 504 " ideal model delta sigma weight residual 1.894 1.472 0.422 2.00e-02 2.50e+03 4.46e+02 ... (remaining 17150 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.82: 580 106.82 - 113.75: 9647 113.75 - 120.69: 7346 120.69 - 127.63: 5642 127.63 - 134.56: 240 Bond angle restraints: 23455 Sorted by residual: angle pdb=" C9 Y82 C 504 " pdb=" C7 Y82 C 504 " pdb=" N2 Y82 C 504 " ideal model delta sigma weight residual 67.36 125.55 -58.19 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C9 Y82 A 504 " pdb=" C7 Y82 A 504 " pdb=" N2 Y82 A 504 " ideal model delta sigma weight residual 67.36 125.54 -58.18 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C9 Y82 E 501 " pdb=" C7 Y82 E 501 " pdb=" N2 Y82 E 501 " ideal model delta sigma weight residual 67.36 125.52 -58.16 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C9 Y82 D 504 " pdb=" C7 Y82 D 504 " pdb=" N2 Y82 D 504 " ideal model delta sigma weight residual 67.36 125.50 -58.14 3.00e+00 1.11e-01 3.76e+02 angle pdb=" C9 Y82 B 504 " pdb=" C7 Y82 B 504 " pdb=" N2 Y82 B 504 " ideal model delta sigma weight residual 67.36 125.49 -58.13 3.00e+00 1.11e-01 3.76e+02 ... (remaining 23450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.81: 9925 28.81 - 57.62: 340 57.62 - 86.44: 30 86.44 - 115.25: 5 115.25 - 144.06: 5 Dihedral angle restraints: 10305 sinusoidal: 4410 harmonic: 5895 Sorted by residual: dihedral pdb=" CB CYS E 135 " pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " pdb=" CB CYS E 149 " ideal model delta sinusoidal sigma weight residual 93.00 131.99 -38.99 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 131.99 -38.99 1 1.00e+01 1.00e-02 2.14e+01 dihedral pdb=" CB CYS C 135 " pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 131.98 -38.98 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 10302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2362 0.077 - 0.153: 348 0.153 - 0.230: 20 0.230 - 0.306: 5 0.306 - 0.383: 15 Chirality restraints: 2750 Sorted by residual: chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 82 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C1 NAG E 502 " pdb=" ND2 ASN E 82 " pdb=" C2 NAG E 502 " pdb=" O5 NAG E 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 2747 not shown) Planarity restraints: 2865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " 0.078 2.00e-02 2.50e+03 6.45e-02 5.21e+01 pdb=" C7 NAG B 501 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " 0.059 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.078 2.00e-02 2.50e+03 6.45e-02 5.21e+01 pdb=" C7 NAG D 501 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.059 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 501 " 0.078 2.00e-02 2.50e+03 6.44e-02 5.19e+01 pdb=" C7 NAG C 501 " -0.021 2.00e-02 2.50e+03 pdb=" C8 NAG C 501 " 0.059 2.00e-02 2.50e+03 pdb=" N2 NAG C 501 " -0.103 2.00e-02 2.50e+03 pdb=" O7 NAG C 501 " -0.013 2.00e-02 2.50e+03 ... (remaining 2862 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 6633 2.92 - 3.42: 16657 3.42 - 3.91: 26294 3.91 - 4.41: 28860 4.41 - 4.90: 46955 Nonbonded interactions: 125399 Sorted by model distance: nonbonded pdb=" NE ARG D 65 " pdb=" C5 Y82 D 504 " model vdw 2.428 3.420 nonbonded pdb=" NE ARG C 65 " pdb=" C5 Y82 C 504 " model vdw 2.429 3.420 nonbonded pdb=" NE ARG B 65 " pdb=" C5 Y82 B 504 " model vdw 2.430 3.420 nonbonded pdb=" NH2 ARG A 410 " pdb=" O GLU B 405 " model vdw 2.453 2.520 nonbonded pdb=" NE ARG A 65 " pdb=" C5 Y82 A 504 " model vdw 2.454 3.420 ... (remaining 125394 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 465 or resid 502 through 503)) } 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.600 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 45.320 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.015 0.424 17155 Z= 0.990 Angle : 1.495 58.192 23455 Z= 0.660 Chirality : 0.058 0.383 2750 Planarity : 0.006 0.065 2850 Dihedral : 14.881 144.062 6450 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % 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: -1.60 (0.19), residues: 1955 helix: 0.24 (0.19), residues: 740 sheet: -1.06 (0.25), residues: 430 loop : -2.30 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 63 HIS 0.003 0.001 HIS A 118 PHE 0.038 0.002 PHE D 287 TYR 0.010 0.002 TYR E 207 ARG 0.012 0.001 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.008 Fit side-chains REVERT: A 254 PHE cc_start: 0.7595 (m-10) cc_final: 0.7328 (t80) REVERT: B 254 PHE cc_start: 0.7747 (m-10) cc_final: 0.7227 (t80) REVERT: C 254 PHE cc_start: 0.7735 (m-10) cc_final: 0.7278 (t80) REVERT: D 254 PHE cc_start: 0.8015 (m-10) cc_final: 0.7421 (t80) REVERT: E 254 PHE cc_start: 0.7806 (m-10) cc_final: 0.7212 (t80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.2336 time to fit residues: 33.5072 Evaluate side-chains 55 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.0270 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN B 124 GLN C 124 GLN D 124 GLN E 124 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 17155 Z= 0.302 Angle : 1.247 48.640 23455 Z= 0.472 Chirality : 0.044 0.315 2750 Planarity : 0.004 0.049 2850 Dihedral : 10.968 163.958 2560 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.22 % Allowed : 7.75 % Favored : 92.03 % 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: -0.64 (0.20), residues: 1955 helix: 1.32 (0.19), residues: 770 sheet: -1.22 (0.24), residues: 435 loop : -1.75 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 156 HIS 0.002 0.001 HIS B 158 PHE 0.020 0.002 PHE A 287 TYR 0.013 0.001 TYR D 441 ARG 0.004 0.000 ARG D 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.961 Fit side-chains REVERT: B 254 PHE cc_start: 0.7562 (m-10) cc_final: 0.7186 (t80) REVERT: C 254 PHE cc_start: 0.7347 (m-10) cc_final: 0.7053 (t80) REVERT: D 254 PHE cc_start: 0.7820 (m-10) cc_final: 0.7307 (t80) REVERT: E 254 PHE cc_start: 0.7483 (m-10) cc_final: 0.6985 (t80) outliers start: 4 outliers final: 2 residues processed: 77 average time/residue: 0.2296 time to fit residues: 30.8082 Evaluate side-chains 62 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain C residue 55 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS B 118 HIS C 118 HIS D 118 HIS E 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 17155 Z= 0.416 Angle : 1.291 49.001 23455 Z= 0.498 Chirality : 0.045 0.323 2750 Planarity : 0.004 0.042 2850 Dihedral : 10.943 165.774 2560 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.03 % Allowed : 11.49 % Favored : 87.48 % 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: -0.48 (0.20), residues: 1955 helix: 1.49 (0.19), residues: 765 sheet: -1.12 (0.23), residues: 445 loop : -1.71 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 156 HIS 0.003 0.001 HIS C 18 PHE 0.019 0.003 PHE A 287 TYR 0.016 0.002 TYR D 64 ARG 0.003 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 2.177 Fit side-chains REVERT: A 411 HIS cc_start: 0.5383 (p90) cc_final: 0.5030 (p90) REVERT: B 442 LEU cc_start: 0.7439 (mt) cc_final: 0.7210 (pp) outliers start: 19 outliers final: 10 residues processed: 88 average time/residue: 0.2391 time to fit residues: 35.8745 Evaluate side-chains 71 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 1.9990 chunk 133 optimal weight: 0.0010 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- 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: 0.8223 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 17155 Z= 0.275 Angle : 1.235 49.279 23455 Z= 0.461 Chirality : 0.043 0.318 2750 Planarity : 0.003 0.039 2850 Dihedral : 10.578 164.006 2560 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.03 % Allowed : 13.60 % Favored : 85.37 % 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: -0.31 (0.20), residues: 1955 helix: 1.71 (0.19), residues: 765 sheet: -1.10 (0.23), residues: 420 loop : -1.65 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 156 HIS 0.002 0.001 HIS C 411 PHE 0.019 0.001 PHE C 287 TYR 0.014 0.001 TYR B 64 ARG 0.002 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 68 time to evaluate : 2.062 Fit side-chains revert: symmetry clash REVERT: A 411 HIS cc_start: 0.5546 (p90) cc_final: 0.5303 (p90) REVERT: C 103 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.6926 (m-10) outliers start: 19 outliers final: 7 residues processed: 81 average time/residue: 0.2246 time to fit residues: 31.6341 Evaluate side-chains 71 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 177 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 0.0040 chunk 77 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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: 0.8196 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 17155 Z= 0.245 Angle : 1.219 49.305 23455 Z= 0.451 Chirality : 0.042 0.309 2750 Planarity : 0.003 0.036 2850 Dihedral : 10.331 164.000 2560 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.03 % Allowed : 14.74 % Favored : 84.23 % 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: -0.11 (0.20), residues: 1955 helix: 1.85 (0.19), residues: 765 sheet: -0.87 (0.23), residues: 440 loop : -1.60 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.000 HIS A 119 PHE 0.019 0.001 PHE D 287 TYR 0.014 0.001 TYR D 67 ARG 0.002 0.000 ARG E 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 2.146 Fit side-chains REVERT: A 411 HIS cc_start: 0.5514 (p90) cc_final: 0.5298 (p90) REVERT: B 442 LEU cc_start: 0.7394 (mt) cc_final: 0.7112 (pp) REVERT: C 442 LEU cc_start: 0.7521 (mt) cc_final: 0.7204 (pp) REVERT: D 442 LEU cc_start: 0.7301 (mt) cc_final: 0.7035 (pp) REVERT: E 411 HIS cc_start: 0.5532 (p90) cc_final: 0.5265 (p-80) outliers start: 19 outliers final: 11 residues processed: 80 average time/residue: 0.2454 time to fit residues: 33.8680 Evaluate side-chains 70 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 0.3980 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 188 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.0170 chunk 99 optimal weight: 8.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- 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: 0.8195 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 17155 Z= 0.248 Angle : 1.219 49.273 23455 Z= 0.452 Chirality : 0.043 0.297 2750 Planarity : 0.003 0.037 2850 Dihedral : 10.264 164.336 2560 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.30 % Allowed : 15.50 % Favored : 83.20 % 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: -0.03 (0.20), residues: 1955 helix: 1.77 (0.19), residues: 775 sheet: -0.77 (0.23), residues: 440 loop : -1.47 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 156 HIS 0.003 0.000 HIS B 411 PHE 0.019 0.001 PHE C 287 TYR 0.013 0.001 TYR D 67 ARG 0.002 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 2.059 Fit side-chains REVERT: C 103 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.6879 (m-10) REVERT: D 411 HIS cc_start: 0.5281 (p90) cc_final: 0.4976 (p90) REVERT: E 442 LEU cc_start: 0.7612 (mt) cc_final: 0.7234 (pp) outliers start: 24 outliers final: 14 residues processed: 82 average time/residue: 0.2387 time to fit residues: 34.0178 Evaluate side-chains 75 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.0040 chunk 105 optimal weight: 0.0970 chunk 187 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 17155 Z= 0.236 Angle : 1.210 49.288 23455 Z= 0.446 Chirality : 0.042 0.286 2750 Planarity : 0.003 0.035 2850 Dihedral : 10.180 164.522 2560 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.63 % Allowed : 15.50 % Favored : 82.87 % 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: 0.01 (0.20), residues: 1955 helix: 1.79 (0.18), residues: 780 sheet: -0.74 (0.23), residues: 440 loop : -1.45 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 68 HIS 0.004 0.000 HIS E 411 PHE 0.016 0.001 PHE D 287 TYR 0.013 0.001 TYR C 67 ARG 0.004 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 67 time to evaluate : 1.854 Fit side-chains revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7301 (pp) REVERT: B 55 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.9101 (p0) REVERT: C 103 PHE cc_start: 0.7428 (OUTLIER) cc_final: 0.6750 (m-10) REVERT: C 442 LEU cc_start: 0.7478 (mt) cc_final: 0.7174 (pp) REVERT: D 411 HIS cc_start: 0.5484 (p90) cc_final: 0.5101 (p90) outliers start: 30 outliers final: 16 residues processed: 90 average time/residue: 0.2338 time to fit residues: 36.0677 Evaluate side-chains 79 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 60 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 461 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 0.0070 chunk 147 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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: 0.8224 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 17155 Z= 0.282 Angle : 1.224 49.179 23455 Z= 0.456 Chirality : 0.043 0.293 2750 Planarity : 0.004 0.037 2850 Dihedral : 10.314 165.013 2560 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.84 % Allowed : 15.34 % Favored : 82.82 % 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: 0.03 (0.20), residues: 1955 helix: 1.94 (0.18), residues: 775 sheet: -0.83 (0.23), residues: 440 loop : -1.53 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 156 HIS 0.002 0.001 HIS D 118 PHE 0.016 0.001 PHE C 287 TYR 0.015 0.001 TYR D 64 ARG 0.002 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 65 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7318 (pp) REVERT: B 465 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.4696 (tt) REVERT: C 103 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6910 (m-10) REVERT: C 411 HIS cc_start: 0.5380 (p90) cc_final: 0.4799 (p90) REVERT: C 442 LEU cc_start: 0.7636 (mt) cc_final: 0.7315 (pp) REVERT: D 411 HIS cc_start: 0.5513 (p90) cc_final: 0.5147 (p90) REVERT: E 465 LEU cc_start: 0.4975 (OUTLIER) cc_final: 0.4739 (pp) outliers start: 34 outliers final: 22 residues processed: 88 average time/residue: 0.2404 time to fit residues: 35.8882 Evaluate side-chains 90 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 64 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 461 TYR Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 175 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.8211 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 17155 Z= 0.255 Angle : 1.217 49.252 23455 Z= 0.450 Chirality : 0.043 0.288 2750 Planarity : 0.003 0.036 2850 Dihedral : 10.244 164.807 2560 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.79 % Allowed : 15.56 % Favored : 82.66 % 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: 0.03 (0.20), residues: 1955 helix: 1.99 (0.18), residues: 775 sheet: -0.91 (0.23), residues: 440 loop : -1.53 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 68 HIS 0.002 0.000 HIS E 411 PHE 0.016 0.001 PHE C 287 TYR 0.014 0.001 TYR D 262 ARG 0.002 0.000 ARG E 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 70 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7398 (pp) REVERT: B 442 LEU cc_start: 0.7430 (mt) cc_final: 0.7139 (pp) REVERT: C 103 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6950 (m-10) REVERT: C 411 HIS cc_start: 0.5282 (p90) cc_final: 0.4783 (p90) REVERT: C 442 LEU cc_start: 0.7573 (mt) cc_final: 0.7294 (pp) REVERT: D 411 HIS cc_start: 0.5688 (p90) cc_final: 0.5328 (p90) REVERT: E 465 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.4934 (pp) outliers start: 33 outliers final: 20 residues processed: 93 average time/residue: 0.2491 time to fit residues: 38.0021 Evaluate side-chains 85 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 461 TYR Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 87 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 119 optimal weight: 0.0980 chunk 94 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8217 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 17155 Z= 0.262 Angle : 1.227 49.205 23455 Z= 0.455 Chirality : 0.043 0.291 2750 Planarity : 0.003 0.036 2850 Dihedral : 10.258 164.982 2560 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.36 % Allowed : 16.21 % Favored : 82.44 % 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: 0.07 (0.20), residues: 1955 helix: 2.05 (0.18), residues: 775 sheet: -0.97 (0.23), residues: 440 loop : -1.49 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 156 HIS 0.002 0.001 HIS E 118 PHE 0.015 0.001 PHE C 287 TYR 0.013 0.001 TYR D 262 ARG 0.002 0.000 ARG B 410 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7432 (pp) REVERT: B 442 LEU cc_start: 0.7455 (mt) cc_final: 0.7144 (pp) REVERT: C 103 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: C 411 HIS cc_start: 0.5200 (p90) cc_final: 0.4712 (p90) REVERT: C 442 LEU cc_start: 0.7583 (mt) cc_final: 0.7301 (pp) REVERT: D 411 HIS cc_start: 0.5627 (p90) cc_final: 0.5403 (p90) REVERT: E 465 LEU cc_start: 0.5436 (OUTLIER) cc_final: 0.5086 (pp) outliers start: 25 outliers final: 21 residues processed: 79 average time/residue: 0.2657 time to fit residues: 36.2728 Evaluate side-chains 87 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 63 time to evaluate : 2.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 461 TYR Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 461 TYR Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 116 TYR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 461 TYR Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 461 TYR Chi-restraints excluded: chain E residue 55 ASN Chi-restraints excluded: chain E residue 235 MET Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 461 TYR Chi-restraints excluded: chain E residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.0270 chunk 47 optimal weight: 0.1980 chunk 142 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.096467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.063318 restraints weight = 56630.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.064879 restraints weight = 30824.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.065782 restraints weight = 21625.957| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 17155 Z= 0.251 Angle : 1.222 49.252 23455 Z= 0.451 Chirality : 0.043 0.287 2750 Planarity : 0.003 0.036 2850 Dihedral : 10.202 164.903 2560 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.46 % Allowed : 16.37 % Favored : 82.17 % 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: 0.08 (0.20), residues: 1955 helix: 2.11 (0.18), residues: 770 sheet: -0.98 (0.23), residues: 440 loop : -1.51 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 68 HIS 0.002 0.000 HIS E 118 PHE 0.015 0.001 PHE E 287 TYR 0.014 0.001 TYR D 262 ARG 0.004 0.000 ARG B 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2374.30 seconds wall clock time: 44 minutes 57.24 seconds (2697.24 seconds total)