Starting phenix.real_space_refine on Tue May 13 17:51:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5f_38068/05_2025/8x5f_38068_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5f_38068/05_2025/8x5f_38068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x5f_38068/05_2025/8x5f_38068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5f_38068/05_2025/8x5f_38068.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5f_38068/05_2025/8x5f_38068_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5f_38068/05_2025/8x5f_38068_neut_trim.cif" } resolution = 2.96 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= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 40 5.16 5 C 7212 2.51 5 N 1669 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10843 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5024 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 5020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5020 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 594} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 399 Unusual residues: {'CLR': 1, 'IHP': 1, 'PO4': 4, 'POV': 15} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 465 Unresolved non-hydrogen angles: 564 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-2': 10, 'POV:plan-1': 11} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 396 Unusual residues: {'CLR': 1, 'IHP': 1, 'PO4': 4, 'POV': 15} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 468 Unresolved non-hydrogen angles: 567 Unresolved non-hydrogen dihedrals: 419 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 9, 'POV:plan-1': 11} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 7.21, per 1000 atoms: 0.66 Number of scatterers: 10843 At special positions: 0 Unit cell: (111.35, 128.35, 102, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 26 15.00 O 1896 8.00 N 1669 7.00 C 7212 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " 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 Time building additional restraints: 2.75 Conformation dependent library (CDL) restraints added in 1.4 seconds 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.775A pdb=" N HIS A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 19 removed outlier: 5.481A pdb=" N LYS A 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR A 19 " --> pdb=" O ARG A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 35 removed outlier: 3.514A pdb=" N PHE A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 53 through 103 removed outlier: 3.525A pdb=" N LYS A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 168 Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.633A pdb=" N ASP A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 189 through 206 removed outlier: 3.728A pdb=" N GLN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.572A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 removed outlier: 3.564A pdb=" N ARG A 236 " --> pdb=" O TRP A 232 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.935A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.535A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 removed outlier: 3.825A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.568A pdb=" N PHE A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 419 removed outlier: 4.105A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 removed outlier: 3.515A pdb=" N ILE A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Proline residue: A 455 - end of helix Processing helix chain 'A' and resid 475 through 502 removed outlier: 4.493A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 502 " --> pdb=" O THR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 532 removed outlier: 3.647A pdb=" N PHE A 510 " --> pdb=" O ASP A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 580 removed outlier: 3.816A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 577 " --> pdb=" O TRP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 620 removed outlier: 3.658A pdb=" N ILE A 591 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.748A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN A 619 " --> pdb=" O GLU A 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 11 removed outlier: 3.775A pdb=" N HIS B 6 " --> pdb=" O LYS B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 19 removed outlier: 5.221A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.514A pdb=" N PHE B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 51 removed outlier: 3.732A pdb=" N VAL B 47 " --> pdb=" O ASP B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 103 removed outlier: 3.525A pdb=" N LYS B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 93 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 168 removed outlier: 3.513A pdb=" N ARG B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.632A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 189 through 206 removed outlier: 3.728A pdb=" N GLN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.572A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 3.565A pdb=" N ARG B 236 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.935A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.535A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 336 removed outlier: 3.825A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.568A pdb=" N PHE B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 419 removed outlier: 4.104A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 475 through 502 removed outlier: 4.494A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 532 removed outlier: 3.647A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 580 removed outlier: 3.816A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 575 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 577 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 620 removed outlier: 3.658A pdb=" N ILE B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.748A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 2043 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: 3.18 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1572 1.31 - 1.43: 3167 1.43 - 1.56: 6253 1.56 - 1.69: 47 1.69 - 1.82: 56 Bond restraints: 11095 Sorted by residual: bond pdb=" C31 POV A 713 " pdb=" O32 POV A 713 " ideal model delta sigma weight residual 1.206 1.402 -0.196 2.00e-02 2.50e+03 9.56e+01 bond pdb=" C31 POV A 711 " pdb=" O32 POV A 711 " ideal model delta sigma weight residual 1.206 1.401 -0.195 2.00e-02 2.50e+03 9.54e+01 bond pdb=" C31 POV A 717 " pdb=" O32 POV A 717 " ideal model delta sigma weight residual 1.206 1.400 -0.194 2.00e-02 2.50e+03 9.44e+01 bond pdb=" C31 POV B1110 " pdb=" O32 POV B1110 " ideal model delta sigma weight residual 1.206 1.399 -0.193 2.00e-02 2.50e+03 9.35e+01 bond pdb=" C31 POV B1112 " pdb=" O32 POV B1112 " ideal model delta sigma weight residual 1.206 1.398 -0.192 2.00e-02 2.50e+03 9.24e+01 ... (remaining 11090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 14523 3.84 - 7.68: 346 7.68 - 11.52: 52 11.52 - 15.36: 2 15.36 - 19.20: 4 Bond angle restraints: 14927 Sorted by residual: angle pdb=" C28 POV A 718 " pdb=" C29 POV A 718 " pdb="C210 POV A 718 " ideal model delta sigma weight residual 127.79 108.59 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" C29 POV A 718 " pdb="C210 POV A 718 " pdb="C211 POV A 718 " ideal model delta sigma weight residual 127.67 108.56 19.11 3.00e+00 1.11e-01 4.06e+01 angle pdb=" C28 POV B1107 " pdb=" C29 POV B1107 " pdb="C210 POV B1107 " ideal model delta sigma weight residual 127.79 108.81 18.98 3.00e+00 1.11e-01 4.00e+01 angle pdb=" N SER A 93 " pdb=" CA SER A 93 " pdb=" C SER A 93 " ideal model delta sigma weight residual 111.28 118.12 -6.84 1.09e+00 8.42e-01 3.94e+01 angle pdb=" N SER B 93 " pdb=" CA SER B 93 " pdb=" C SER B 93 " ideal model delta sigma weight residual 111.28 118.11 -6.83 1.09e+00 8.42e-01 3.93e+01 ... (remaining 14922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 6376 31.27 - 62.53: 284 62.53 - 93.80: 30 93.80 - 125.07: 5 125.07 - 156.34: 4 Dihedral angle restraints: 6699 sinusoidal: 3053 harmonic: 3646 Sorted by residual: dihedral pdb=" CB CYS B 415 " pdb=" SG CYS B 415 " pdb=" SG CYS B 440 " pdb=" CB CYS B 440 " ideal model delta sinusoidal sigma weight residual 93.00 163.35 -70.35 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" C VAL B 626 " pdb=" N VAL B 626 " pdb=" CA VAL B 626 " pdb=" CB VAL B 626 " ideal model delta harmonic sigma weight residual -122.00 -135.65 13.65 0 2.50e+00 1.60e-01 2.98e+01 dihedral pdb=" N VAL B 626 " pdb=" C VAL B 626 " pdb=" CA VAL B 626 " pdb=" CB VAL B 626 " ideal model delta harmonic sigma weight residual 123.40 135.07 -11.67 0 2.50e+00 1.60e-01 2.18e+01 ... (remaining 6696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1383 0.076 - 0.151: 152 0.151 - 0.227: 22 0.227 - 0.302: 12 0.302 - 0.378: 3 Chirality restraints: 1572 Sorted by residual: chirality pdb=" CA THR B 582 " pdb=" N THR B 582 " pdb=" C THR B 582 " pdb=" CB THR B 582 " both_signs ideal model delta sigma weight residual False 2.53 2.15 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA VAL B 626 " pdb=" N VAL B 626 " pdb=" C VAL B 626 " pdb=" CB VAL B 626 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA HIS B 441 " pdb=" N HIS B 441 " pdb=" C HIS B 441 " pdb=" CB HIS B 441 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1569 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B1107 " -0.152 2.00e-02 2.50e+03 2.51e-01 6.30e+02 pdb=" C29 POV B1107 " 0.321 2.00e-02 2.50e+03 pdb="C210 POV B1107 " -0.321 2.00e-02 2.50e+03 pdb="C211 POV B1107 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 718 " 0.141 2.00e-02 2.50e+03 2.20e-01 4.82e+02 pdb=" C29 POV A 718 " -0.277 2.00e-02 2.50e+03 pdb="C210 POV A 718 " 0.277 2.00e-02 2.50e+03 pdb="C211 POV A 718 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 35 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C GLN B 35 " 0.064 2.00e-02 2.50e+03 pdb=" O GLN B 35 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 36 " -0.022 2.00e-02 2.50e+03 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 222 2.70 - 3.25: 10150 3.25 - 3.80: 16045 3.80 - 4.35: 20221 4.35 - 4.90: 35841 Nonbonded interactions: 82479 Sorted by model distance: nonbonded pdb=" N GLN A 227 " pdb=" OE1 GLN A 227 " model vdw 2.149 3.120 nonbonded pdb=" OG SER B 497 " pdb=" O THR B 582 " model vdw 2.259 3.040 nonbonded pdb=" O ARG B 217 " pdb=" NH1 ARG B 308 " model vdw 2.304 3.120 nonbonded pdb=" O ARG A 217 " pdb=" NH1 ARG A 308 " model vdw 2.305 3.120 nonbonded pdb=" OG SER A 497 " pdb=" O THR A 582 " model vdw 2.305 3.040 ... (remaining 82474 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 1 through 441 or (resid 442 through 443 and (name N or nam \ e CA or name C or name O or name CB )) or resid 444 through 635 or resid 702 thr \ ough 704 or resid 707 or (resid 708 and (name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name O31 or \ name O32 or name C310 or name C311)) or resid 710 or resid 712 through 716 or ( \ resid 719 and (name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O31 or name O32 or name C310 or \ name C311 or name C312 or name C313 or name C314)) or resid 720 or (resid 721 an \ d (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C2 \ 5 or name C26 or name C27 or name C28 or name C3 or name C31 or name C32 or name \ C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P )))) selection = (chain 'B' and (resid 1 through 635 or resid 1102 through 1104 or resid 1107 or \ (resid 1108 and (name C31 or name C32 or name C33 or name C34 or name C35 or nam \ e C36 or name C37 or name C38 or name C39 or name O31 or name O32 or name C310 o \ r name C311)) or resid 1110 or resid 1112 or (resid 1113 and (name C31 or name C \ 32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or na \ me C39 or name O31 or name O32 or name C310 or name C311 or name C312)) or resid \ 1114 through 1116 or resid 1119 or (resid 1120 and (name N or name C1 or name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or nam \ e C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or \ name C3 or name C31 or name C32 or name C33 or name O11 or name O12 or name O13 \ or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (re \ sid 1121 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C3 or name C31 or name \ C32 or name C33 or name O11 or name O12 or name O13 or name O14 or name O21 or n \ ame O22 or name O31 or name O32 or name P )))) } 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 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: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.230 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.011 0.196 11097 Z= 0.548 Angle : 1.270 19.201 14931 Z= 0.591 Chirality : 0.057 0.378 1572 Planarity : 0.009 0.251 1794 Dihedral : 17.296 156.336 4329 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.77 % Favored : 96.07 % Rotamer: Outliers : 0.67 % Allowed : 2.12 % Favored : 97.21 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 4.76 % 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: 1.88 (0.24), residues: 1220 helix: 2.14 (0.17), residues: 902 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 607 HIS 0.005 0.001 HIS B 313 PHE 0.019 0.002 PHE B 571 TYR 0.035 0.002 TYR B 524 ARG 0.004 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.16941 ( 692) hydrogen bonds : angle 5.03569 ( 2043) SS BOND : bond 0.00247 ( 2) SS BOND : angle 1.86591 ( 4) covalent geometry : bond 0.01054 (11095) covalent geometry : angle 1.26970 (14927) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 175 time to evaluate : 1.226 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 181 average time/residue: 1.3608 time to fit residues: 264.8466 Evaluate side-chains 97 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 626 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 499 HIS B 127 ASN B 452 GLN B 499 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115377 restraints weight = 12446.699| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.37 r_work: 0.3250 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11097 Z= 0.178 Angle : 0.573 7.138 14931 Z= 0.307 Chirality : 0.040 0.141 1572 Planarity : 0.005 0.045 1794 Dihedral : 15.404 139.120 2045 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.80 % Rotamer: Outliers : 3.18 % Allowed : 11.16 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.28 (0.24), residues: 1220 helix: 2.41 (0.17), residues: 916 sheet: None (None), residues: 0 loop : -1.45 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 607 HIS 0.010 0.002 HIS B 441 PHE 0.015 0.002 PHE B 517 TYR 0.027 0.002 TYR B 524 ARG 0.006 0.001 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.07227 ( 692) hydrogen bonds : angle 3.78853 ( 2043) SS BOND : bond 0.00424 ( 2) SS BOND : angle 0.91675 ( 4) covalent geometry : bond 0.00398 (11095) covalent geometry : angle 0.57293 (14927) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 104 time to evaluate : 1.279 Fit side-chains REVERT: A 64 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7961 (mtpp) REVERT: A 529 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 540 ASN cc_start: 0.8397 (p0) cc_final: 0.8152 (p0) REVERT: B 64 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7884 (mtpp) REVERT: B 468 ARG cc_start: 0.7488 (tmt170) cc_final: 0.7240 (tmt170) REVERT: B 540 ASN cc_start: 0.8431 (p0) cc_final: 0.8190 (p0) outliers start: 33 outliers final: 13 residues processed: 121 average time/residue: 1.3130 time to fit residues: 171.3133 Evaluate side-chains 103 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 12 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 36 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.166190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.111036 restraints weight = 12623.135| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.38 r_work: 0.3199 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11097 Z= 0.201 Angle : 0.569 5.991 14931 Z= 0.305 Chirality : 0.041 0.145 1572 Planarity : 0.005 0.041 1794 Dihedral : 14.700 128.232 2044 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 3.27 % Allowed : 13.19 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.23 (0.25), residues: 1220 helix: 2.38 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.48 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 607 HIS 0.008 0.001 HIS B 441 PHE 0.018 0.002 PHE B 571 TYR 0.020 0.002 TYR A 524 ARG 0.005 0.001 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.07740 ( 692) hydrogen bonds : angle 3.70840 ( 2043) SS BOND : bond 0.00383 ( 2) SS BOND : angle 1.00787 ( 4) covalent geometry : bond 0.00472 (11095) covalent geometry : angle 0.56885 (14927) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 1.260 Fit side-chains REVERT: A 64 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7902 (mtpp) REVERT: A 159 ILE cc_start: 0.7781 (tp) cc_final: 0.7550 (tp) REVERT: A 167 LEU cc_start: 0.6350 (mp) cc_final: 0.6019 (tt) REVERT: A 309 SER cc_start: 0.8074 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 529 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7943 (t0) REVERT: A 540 ASN cc_start: 0.8350 (p0) cc_final: 0.8116 (p0) REVERT: B 64 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7882 (mtpp) REVERT: B 167 LEU cc_start: 0.6373 (mp) cc_final: 0.6047 (tt) REVERT: B 211 ARG cc_start: 0.6653 (ttt90) cc_final: 0.6438 (ttt180) REVERT: B 529 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7973 (t0) REVERT: B 540 ASN cc_start: 0.8429 (p0) cc_final: 0.8156 (p0) outliers start: 34 outliers final: 15 residues processed: 110 average time/residue: 1.2569 time to fit residues: 149.6996 Evaluate side-chains 107 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.0050 chunk 84 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 499 HIS B 163 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.112938 restraints weight = 12547.288| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.34 r_work: 0.3210 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11097 Z= 0.179 Angle : 0.517 6.134 14931 Z= 0.280 Chirality : 0.039 0.131 1572 Planarity : 0.004 0.038 1794 Dihedral : 14.199 115.045 2044 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.38 % Favored : 97.46 % Rotamer: Outliers : 3.27 % Allowed : 14.53 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.32 (0.25), residues: 1220 helix: 2.45 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.49 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 607 HIS 0.008 0.001 HIS B 441 PHE 0.016 0.002 PHE A 517 TYR 0.016 0.002 TYR B 496 ARG 0.008 0.001 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.07054 ( 692) hydrogen bonds : angle 3.60827 ( 2043) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.83357 ( 4) covalent geometry : bond 0.00416 (11095) covalent geometry : angle 0.51732 (14927) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 1.102 Fit side-chains REVERT: A 159 ILE cc_start: 0.7738 (tp) cc_final: 0.7526 (tp) REVERT: A 167 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5995 (tt) REVERT: A 309 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7919 (p) REVERT: A 529 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (t0) REVERT: A 540 ASN cc_start: 0.8448 (p0) cc_final: 0.8247 (p0) REVERT: A 579 ILE cc_start: 0.7119 (OUTLIER) cc_final: 0.6789 (mp) REVERT: B 17 LYS cc_start: 0.8052 (mttt) cc_final: 0.7435 (tptp) REVERT: B 167 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.6077 (tt) REVERT: B 199 GLU cc_start: 0.6329 (pt0) cc_final: 0.6086 (pt0) REVERT: B 345 TYR cc_start: 0.8459 (p90) cc_final: 0.8257 (p90) REVERT: B 529 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8006 (t0) REVERT: B 540 ASN cc_start: 0.8389 (p0) cc_final: 0.8135 (p0) REVERT: B 579 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6791 (mp) outliers start: 34 outliers final: 15 residues processed: 115 average time/residue: 1.2374 time to fit residues: 153.8857 Evaluate side-chains 108 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 82 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 113 optimal weight: 0.0470 chunk 120 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 110 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117611 restraints weight = 12609.214| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.20 r_work: 0.3252 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11097 Z= 0.125 Angle : 0.459 6.232 14931 Z= 0.249 Chirality : 0.036 0.122 1572 Planarity : 0.004 0.038 1794 Dihedral : 13.300 109.858 2044 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.30 % Favored : 97.54 % Rotamer: Outliers : 2.50 % Allowed : 15.69 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.78 (0.25), residues: 1220 helix: 2.78 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.31 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 607 HIS 0.008 0.001 HIS B 441 PHE 0.012 0.001 PHE A 460 TYR 0.022 0.001 TYR B 496 ARG 0.006 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.05668 ( 692) hydrogen bonds : angle 3.40084 ( 2043) SS BOND : bond 0.00191 ( 2) SS BOND : angle 0.71123 ( 4) covalent geometry : bond 0.00261 (11095) covalent geometry : angle 0.45846 (14927) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.164 Fit side-chains REVERT: A 147 ASN cc_start: 0.7738 (m-40) cc_final: 0.7350 (m-40) REVERT: A 529 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: B 17 LYS cc_start: 0.7939 (mttt) cc_final: 0.7280 (tptp) REVERT: B 147 ASN cc_start: 0.7674 (m-40) cc_final: 0.7291 (m-40) REVERT: B 529 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: B 540 ASN cc_start: 0.8189 (p0) cc_final: 0.7896 (p0) outliers start: 26 outliers final: 14 residues processed: 107 average time/residue: 1.1767 time to fit residues: 137.0182 Evaluate side-chains 102 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 45 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 35 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 14 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 192 ASN B 146 GLN B 192 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118570 restraints weight = 12723.326| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.22 r_work: 0.3277 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11097 Z= 0.120 Angle : 0.456 7.754 14931 Z= 0.247 Chirality : 0.035 0.128 1572 Planarity : 0.004 0.039 1794 Dihedral : 12.862 110.979 2040 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 2.60 % Allowed : 14.82 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.97 (0.25), residues: 1220 helix: 2.94 (0.17), residues: 916 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 607 HIS 0.007 0.001 HIS B 441 PHE 0.011 0.001 PHE A 460 TYR 0.023 0.001 TYR A 496 ARG 0.008 0.000 ARG B 176 Details of bonding type rmsd hydrogen bonds : bond 0.05338 ( 692) hydrogen bonds : angle 3.33150 ( 2043) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.65063 ( 4) covalent geometry : bond 0.00245 (11095) covalent geometry : angle 0.45641 (14927) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.089 Fit side-chains REVERT: A 147 ASN cc_start: 0.7869 (m-40) cc_final: 0.7466 (m-40) REVERT: A 529 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: B 17 LYS cc_start: 0.7952 (mttt) cc_final: 0.7309 (tptp) REVERT: B 147 ASN cc_start: 0.7727 (m-40) cc_final: 0.7343 (m-40) REVERT: B 529 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7475 (m-30) REVERT: B 540 ASN cc_start: 0.8209 (p0) cc_final: 0.7941 (p0) outliers start: 27 outliers final: 11 residues processed: 113 average time/residue: 1.1865 time to fit residues: 145.8831 Evaluate side-chains 101 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.171648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.128147 restraints weight = 12893.819| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.99 r_work: 0.3240 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11097 Z= 0.147 Angle : 0.511 9.915 14931 Z= 0.269 Chirality : 0.037 0.154 1572 Planarity : 0.004 0.037 1794 Dihedral : 12.967 112.456 2040 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 3.08 % Allowed : 15.30 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.80 (0.25), residues: 1220 helix: 2.78 (0.17), residues: 920 sheet: None (None), residues: 0 loop : -1.30 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 607 HIS 0.007 0.001 HIS B 441 PHE 0.014 0.001 PHE B 517 TYR 0.026 0.002 TYR B 496 ARG 0.008 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.06121 ( 692) hydrogen bonds : angle 3.42649 ( 2043) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.59918 ( 4) covalent geometry : bond 0.00331 (11095) covalent geometry : angle 0.51131 (14927) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 1.564 Fit side-chains REVERT: A 147 ASN cc_start: 0.8458 (m-40) cc_final: 0.8028 (m-40) REVERT: A 529 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: B 17 LYS cc_start: 0.8210 (mttt) cc_final: 0.7642 (tptp) REVERT: B 147 ASN cc_start: 0.8394 (m-40) cc_final: 0.7974 (m-40) REVERT: B 529 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7811 (m-30) REVERT: B 540 ASN cc_start: 0.8358 (p0) cc_final: 0.8141 (p0) outliers start: 32 outliers final: 21 residues processed: 111 average time/residue: 1.1691 time to fit residues: 142.4227 Evaluate side-chains 111 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 550 GLU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.167604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.123748 restraints weight = 12719.696| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.74 r_work: 0.3228 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11097 Z= 0.210 Angle : 0.590 10.946 14931 Z= 0.308 Chirality : 0.041 0.139 1572 Planarity : 0.004 0.038 1794 Dihedral : 13.651 114.573 2040 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.52 % Favored : 96.31 % Rotamer: Outliers : 2.79 % Allowed : 15.69 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.37 (0.24), residues: 1220 helix: 2.47 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.40 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 607 HIS 0.007 0.001 HIS B 441 PHE 0.018 0.002 PHE B 517 TYR 0.029 0.002 TYR B 496 ARG 0.008 0.001 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.07541 ( 692) hydrogen bonds : angle 3.65288 ( 2043) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.62938 ( 4) covalent geometry : bond 0.00501 (11095) covalent geometry : angle 0.58983 (14927) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 1.177 Fit side-chains REVERT: A 309 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8149 (p) REVERT: A 529 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8114 (t0) REVERT: B 17 LYS cc_start: 0.8248 (mttt) cc_final: 0.7655 (tptp) REVERT: B 529 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8131 (t0) REVERT: B 540 ASN cc_start: 0.8453 (p0) cc_final: 0.8188 (p0) outliers start: 29 outliers final: 20 residues processed: 111 average time/residue: 1.1766 time to fit residues: 142.8540 Evaluate side-chains 105 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 28 MET Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 529 ASP Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.169989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.125030 restraints weight = 12885.400| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.82 r_work: 0.3241 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11097 Z= 0.164 Angle : 0.545 11.900 14931 Z= 0.286 Chirality : 0.038 0.155 1572 Planarity : 0.004 0.038 1794 Dihedral : 13.205 111.844 2040 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.54 % Favored : 97.30 % Rotamer: Outliers : 2.60 % Allowed : 16.36 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.50 (0.25), residues: 1220 helix: 2.57 (0.17), residues: 918 sheet: None (None), residues: 0 loop : -1.38 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 607 HIS 0.007 0.001 HIS B 441 PHE 0.014 0.001 PHE A 517 TYR 0.030 0.002 TYR A 496 ARG 0.009 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.06525 ( 692) hydrogen bonds : angle 3.53021 ( 2043) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.66970 ( 4) covalent geometry : bond 0.00375 (11095) covalent geometry : angle 0.54528 (14927) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.101 Fit side-chains REVERT: A 309 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.8110 (p) REVERT: A 498 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7882 (t) REVERT: B 17 LYS cc_start: 0.8293 (mttt) cc_final: 0.7716 (tptp) REVERT: B 540 ASN cc_start: 0.8459 (p0) cc_final: 0.8197 (p0) outliers start: 27 outliers final: 19 residues processed: 104 average time/residue: 1.1002 time to fit residues: 125.1412 Evaluate side-chains 108 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 192 ASN B 146 GLN B 192 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.169006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125155 restraints weight = 12743.879| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.77 r_work: 0.3259 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11097 Z= 0.160 Angle : 0.548 12.267 14931 Z= 0.286 Chirality : 0.038 0.155 1572 Planarity : 0.004 0.040 1794 Dihedral : 13.090 112.132 2040 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 2.21 % Allowed : 16.27 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.55 (0.25), residues: 1220 helix: 2.61 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -1.27 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 607 HIS 0.007 0.001 HIS B 441 PHE 0.014 0.001 PHE A 517 TYR 0.026 0.002 TYR B 496 ARG 0.009 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.06447 ( 692) hydrogen bonds : angle 3.52112 ( 2043) SS BOND : bond 0.00111 ( 2) SS BOND : angle 0.69011 ( 4) covalent geometry : bond 0.00365 (11095) covalent geometry : angle 0.54775 (14927) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2440 Ramachandran restraints generated. 1220 Oldfield, 0 Emsley, 1220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.099 Fit side-chains REVERT: A 147 ASN cc_start: 0.8545 (m-40) cc_final: 0.8130 (m-40) REVERT: A 309 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 17 LYS cc_start: 0.8290 (mttt) cc_final: 0.7721 (tptp) REVERT: B 147 ASN cc_start: 0.8497 (m-40) cc_final: 0.8090 (m-40) REVERT: B 540 ASN cc_start: 0.8449 (p0) cc_final: 0.8205 (p0) outliers start: 23 outliers final: 21 residues processed: 105 average time/residue: 1.2023 time to fit residues: 137.0555 Evaluate side-chains 105 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 156 PHE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 588 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.173186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.129835 restraints weight = 12627.994| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.07 r_work: 0.3321 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11097 Z= 0.122 Angle : 0.505 11.897 14931 Z= 0.265 Chirality : 0.036 0.173 1572 Planarity : 0.004 0.038 1794 Dihedral : 12.450 109.730 2040 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.13 % Favored : 97.70 % Rotamer: Outliers : 1.54 % Allowed : 17.32 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.89 (0.25), residues: 1220 helix: 2.89 (0.17), residues: 910 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 607 HIS 0.006 0.001 HIS B 441 PHE 0.012 0.001 PHE B 460 TYR 0.025 0.001 TYR A 496 ARG 0.009 0.000 ARG A 176 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 692) hydrogen bonds : angle 3.36133 ( 2043) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.70374 ( 4) covalent geometry : bond 0.00255 (11095) covalent geometry : angle 0.50541 (14927) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7164.38 seconds wall clock time: 124 minutes 15.58 seconds (7455.58 seconds total)