Starting phenix.real_space_refine on Wed Jan 15 17:55:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vkj_43319/01_2025/8vkj_43319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vkj_43319/01_2025/8vkj_43319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vkj_43319/01_2025/8vkj_43319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vkj_43319/01_2025/8vkj_43319.map" model { file = "/net/cci-nas-00/data/ceres_data/8vkj_43319/01_2025/8vkj_43319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vkj_43319/01_2025/8vkj_43319.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 6 5.49 5 S 39 5.16 5 C 5685 2.51 5 N 1382 2.21 5 O 1510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8622 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 548, 4243 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 Conformer: "B" Number of residues, atoms: 548, 4243 Classifications: {'peptide': 548} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 26, 'TRANS': 521} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 68 bond proxies already assigned to first conformer: 4350 Chain: "B" Number of atoms: 4168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4168 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 26, 'TRANS': 514} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'ACO': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 93 Unusual residues: {'ACO': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 269 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 269 " occ=0.50 Time building chain proxies: 8.90, per 1000 atoms: 1.03 Number of scatterers: 8622 At special positions: 0 Unit cell: (104.877, 81.3, 104.064, 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 39 16.00 P 6 15.00 O 1510 8.00 N 1382 7.00 C 5685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 107 " distance=2.02 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 462 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 162 " " NAG A 703 " - " ASN A 94 " " NAG B 701 " - " ASN B 162 " " NAG B 703 " - " ASN B 94 " " NAG B 704 " - " ASN B 142 " " NAG C 1 " - " ASN A 142 " Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.5 seconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 5 sheets defined 56.8% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 196 through 228 removed outlier: 3.691A pdb=" N LEU A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 288 through 296 removed outlier: 6.608A pdb=" N TRP A 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 331 Processing helix chain 'A' and resid 334 through 357 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 417 through 437 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.652A pdb=" N LYS A 458 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.794A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 524 removed outlier: 4.026A pdb=" N ASN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 551 removed outlier: 3.685A pdb=" N ILE A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 590 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 606 through 617 Processing helix chain 'A' and resid 632 through 657 Processing helix chain 'B' and resid 191 through 196 Processing helix chain 'B' and resid 197 through 228 removed outlier: 3.661A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 287 Processing helix chain 'B' and resid 288 through 296 removed outlier: 6.551A pdb=" N TRP B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 331 Processing helix chain 'B' and resid 334 through 356 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 438 removed outlier: 3.537A pdb=" N LEU B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.610A pdb=" N LYS B 458 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 476 Processing helix chain 'B' and resid 477 through 480 removed outlier: 3.698A pdb=" N LEU B 480 " --> pdb=" O ASP B 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 477 through 480' Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.178A pdb=" N VAL B 488 " --> pdb=" O SER B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 524 removed outlier: 4.234A pdb=" N ASN B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 551 Processing helix chain 'B' and resid 567 through 590 Proline residue: B 587 - end of helix Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 617 Processing helix chain 'B' and resid 632 through 658 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.137A pdb=" N LEU A 83 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ASN A 169 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.814A pdb=" N VAL A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN A 114 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU A 95 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N CYS A 151 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132 removed outlier: 3.524A pdb=" N SER B 125 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 87 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 167 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 125 through 132 removed outlier: 3.524A pdb=" N SER B 125 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 87 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 167 " --> pdb=" O HIS B 87 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASN B 162 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.717A pdb=" N VAL B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 95 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ASP B 143 " --> pdb=" O GLU B 149 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU B 149 " --> pdb=" O ASP B 143 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1446 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: 2.47 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1373 1.32 - 1.45: 2496 1.45 - 1.57: 4929 1.57 - 1.69: 10 1.69 - 1.82: 53 Bond restraints: 8861 Sorted by residual: bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.522 -0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" N PRO A 419 " pdb=" CD PRO A 419 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.48e+00 bond pdb=" CB PRO A 419 " pdb=" CG PRO A 419 " ideal model delta sigma weight residual 1.492 1.627 -0.135 5.00e-02 4.00e+02 7.27e+00 bond pdb=" N PRO A 419 " pdb=" CA PRO A 419 " ideal model delta sigma weight residual 1.469 1.435 0.033 1.28e-02 6.10e+03 6.81e+00 bond pdb=" CG PRO A 419 " pdb=" CD PRO A 419 " ideal model delta sigma weight residual 1.503 1.423 0.080 3.40e-02 8.65e+02 5.58e+00 ... (remaining 8856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 12080 3.98 - 7.95: 36 7.95 - 11.93: 1 11.93 - 15.91: 1 15.91 - 19.89: 1 Bond angle restraints: 12119 Sorted by residual: angle pdb=" CA PRO A 419 " pdb=" N PRO A 419 " pdb=" CD PRO A 419 " ideal model delta sigma weight residual 112.00 92.11 19.89 1.40e+00 5.10e-01 2.02e+02 angle pdb=" N PRO A 419 " pdb=" CD PRO A 419 " pdb=" CG PRO A 419 " ideal model delta sigma weight residual 103.20 95.41 7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" CA LEU B 411 " pdb=" CB LEU B 411 " pdb=" CG LEU B 411 " ideal model delta sigma weight residual 116.30 129.52 -13.22 3.50e+00 8.16e-02 1.43e+01 angle pdb=" CA PRO A 419 " pdb=" CB PRO A 419 " pdb=" CG PRO A 419 " ideal model delta sigma weight residual 104.50 98.27 6.23 1.90e+00 2.77e-01 1.07e+01 angle pdb=" CA LYS A 529 " pdb=" CB LYS A 529 " pdb=" CG LYS A 529 " ideal model delta sigma weight residual 114.10 120.42 -6.32 2.00e+00 2.50e-01 9.98e+00 ... (remaining 12114 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.38: 4775 22.38 - 44.76: 372 44.76 - 67.13: 72 67.13 - 89.51: 12 89.51 - 111.89: 1 Dihedral angle restraints: 5232 sinusoidal: 2080 harmonic: 3152 Sorted by residual: dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 462 " pdb=" CB CYS A 462 " ideal model delta sinusoidal sigma weight residual 93.00 167.28 -74.28 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS B 443 " pdb=" SG CYS B 443 " pdb=" SG CYS B 462 " pdb=" CB CYS B 462 " ideal model delta sinusoidal sigma weight residual 93.00 163.30 -70.30 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CA GLY A 597 " pdb=" C GLY A 597 " pdb=" N THR A 598 " pdb=" CA THR A 598 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 5229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 844 0.033 - 0.066: 419 0.066 - 0.098: 118 0.098 - 0.131: 33 0.131 - 0.164: 4 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA THR B 598 " pdb=" N THR B 598 " pdb=" C THR B 598 " pdb=" CB THR B 598 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CG LEU B 90 " pdb=" CB LEU B 90 " pdb=" CD1 LEU B 90 " pdb=" CD2 LEU B 90 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA PHE B 621 " pdb=" N PHE B 621 " pdb=" C PHE B 621 " pdb=" CB PHE B 621 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1415 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 418 " 0.114 5.00e-02 4.00e+02 1.55e-01 3.85e+01 pdb=" N PRO A 419 " -0.267 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " 0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 123 " -0.049 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO B 124 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 269 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" C ARG B 269 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG B 269 " -0.013 2.00e-02 2.50e+03 pdb=" N SER B 270 " -0.012 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 757 2.74 - 3.28: 8761 3.28 - 3.82: 15571 3.82 - 4.36: 18266 4.36 - 4.90: 31725 Nonbonded interactions: 75080 Sorted by model distance: nonbonded pdb=" OH TYR B 447 " pdb=" OD2 ASP B 455 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR A 304 " pdb=" OD2 ASP A 307 " model vdw 2.218 3.040 nonbonded pdb=" O ILE B 355 " pdb=" OH TYR B 361 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP B 413 " pdb=" OH TYR B 524 " model vdw 2.240 3.040 nonbonded pdb=" O ILE A 355 " pdb=" OH TYR A 361 " model vdw 2.254 3.040 ... (remaining 75075 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 76 through 144 or (resid 145 through 146 and (name N or na \ me CA or name C or name O or name CB )) or resid 147 or (resid 148 and (name N o \ r name CA or name C or name O or name CB )) or resid 149 through 167 or (resid 1 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 169 through \ 170 or resid 177 through 190 or (resid 191 through 193 and (name N or name CA o \ r name C or name O or name CB )) or resid 194 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 223 or (re \ sid 224 through 266 and (name N or name CA or name C or name O or name CB )) or \ resid 267 through 268 or resid 270 through 336 or (resid 337 and (name N or name \ CA or name C or name O or name CB )) or resid 338 through 400 or (resid 407 thr \ ough 409 and (name N or name CA or name C or name O or name CB )) or resid 410 t \ hrough 528 or (resid 529 and (name N or name CA or name C or name O or name CB ) \ ) or resid 530 through 555 or (resid 556 and (name N or name CA or name C or nam \ e O or name CB )) or resid 557 through 663 or resid 701 through 703)) selection = (chain 'B' and (resid 76 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 through 210 or (resid 211 through 266 a \ nd (name N or name CA or name C or name O or name CB )) or resid 267 through 268 \ or resid 270 through 368 or (resid 369 and (name N or name CA or name C or name \ O or name CB )) or resid 370 through 400 or (resid 407 through 409 and (name N \ or name CA or name C or name O or name CB )) or resid 410 through 663 or resid 7 \ 01 through 703)) } 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=0.50 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: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.360 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 8861 Z= 0.299 Angle : 0.627 19.887 12119 Z= 0.330 Chirality : 0.041 0.164 1418 Planarity : 0.006 0.155 1466 Dihedral : 16.087 111.891 3194 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 0.34 % Allowed : 11.56 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1078 helix: 2.04 (0.22), residues: 525 sheet: -0.39 (0.49), residues: 126 loop : -1.51 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 418 HIS 0.004 0.001 HIS A 614 PHE 0.014 0.001 PHE B 322 TYR 0.014 0.001 TYR B 570 ARG 0.004 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.789 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 1.2141 time to fit residues: 81.2875 Evaluate side-chains 60 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 506 ASN A 614 HIS B 87 HIS B 134 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.143893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.113187 restraints weight = 20081.931| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.30 r_work: 0.3139 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8861 Z= 0.265 Angle : 0.579 7.619 12119 Z= 0.298 Chirality : 0.042 0.160 1418 Planarity : 0.004 0.078 1466 Dihedral : 9.961 77.612 1417 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.17 % Allowed : 10.53 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1078 helix: 2.08 (0.22), residues: 523 sheet: -0.23 (0.50), residues: 122 loop : -1.54 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.016 0.001 PHE B 601 TYR 0.016 0.001 TYR B 570 ARG 0.004 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.899 Fit side-chains REVERT: A 78 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7629 (mmtt) REVERT: A 180 ASP cc_start: 0.7433 (t0) cc_final: 0.6641 (p0) outliers start: 19 outliers final: 9 residues processed: 80 average time/residue: 1.0170 time to fit residues: 88.4909 Evaluate side-chains 73 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 89 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 GLN B 135 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113159 restraints weight = 18511.103| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.13 r_work: 0.3148 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8861 Z= 0.264 Angle : 0.557 6.980 12119 Z= 0.287 Chirality : 0.042 0.160 1418 Planarity : 0.004 0.036 1466 Dihedral : 9.304 67.013 1416 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 2.52 % Allowed : 11.67 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1078 helix: 2.03 (0.22), residues: 531 sheet: -0.39 (0.48), residues: 122 loop : -1.54 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.015 0.001 PHE B 601 TYR 0.016 0.001 TYR B 570 ARG 0.005 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.849 Fit side-chains REVERT: A 78 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7640 (mmtt) REVERT: A 135 HIS cc_start: 0.8249 (OUTLIER) cc_final: 0.7806 (p90) REVERT: A 337 ARG cc_start: 0.7794 (tmt170) cc_final: 0.7476 (ttt-90) REVERT: B 151 CYS cc_start: 0.7628 (p) cc_final: 0.7423 (p) REVERT: B 199 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7572 (mm) REVERT: B 411 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7715 (tt) outliers start: 22 outliers final: 9 residues processed: 82 average time/residue: 0.9238 time to fit residues: 83.1523 Evaluate side-chains 78 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.145900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116941 restraints weight = 17409.231| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.20 r_work: 0.3200 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 8861 Z= 0.329 Angle : 0.591 7.230 12119 Z= 0.302 Chirality : 0.043 0.170 1418 Planarity : 0.004 0.039 1466 Dihedral : 9.202 59.789 1416 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.75 % Allowed : 12.13 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1078 helix: 1.93 (0.22), residues: 531 sheet: -0.54 (0.47), residues: 123 loop : -1.58 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 PHE 0.016 0.002 PHE A 601 TYR 0.018 0.002 TYR B 570 ARG 0.005 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.867 Fit side-chains REVERT: A 78 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7796 (mmtt) REVERT: A 135 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7831 (p90) REVERT: A 180 ASP cc_start: 0.7416 (t0) cc_final: 0.6626 (p0) REVERT: A 337 ARG cc_start: 0.7802 (tmt170) cc_final: 0.7445 (ttt-90) REVERT: B 151 CYS cc_start: 0.7672 (p) cc_final: 0.7470 (p) REVERT: B 199 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7601 (mm) REVERT: B 411 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7775 (tt) outliers start: 24 outliers final: 11 residues processed: 81 average time/residue: 0.9507 time to fit residues: 84.3951 Evaluate side-chains 79 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119310 restraints weight = 14353.022| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.97 r_work: 0.3232 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8861 Z= 0.282 Angle : 0.563 7.486 12119 Z= 0.289 Chirality : 0.042 0.164 1418 Planarity : 0.004 0.036 1466 Dihedral : 8.917 59.990 1416 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.63 % Allowed : 13.16 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1078 helix: 1.97 (0.22), residues: 531 sheet: -0.56 (0.47), residues: 123 loop : -1.57 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.015 0.001 PHE A 601 TYR 0.018 0.001 TYR B 570 ARG 0.005 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.903 Fit side-chains REVERT: A 78 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7730 (mmtt) REVERT: A 135 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7896 (p90) REVERT: A 180 ASP cc_start: 0.7394 (t0) cc_final: 0.6591 (p0) REVERT: A 337 ARG cc_start: 0.7712 (tmt170) cc_final: 0.7343 (ttt-90) REVERT: A 370 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.8033 (mttp) REVERT: A 477 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: A 605 MET cc_start: 0.8588 (mmm) cc_final: 0.8274 (mpp) REVERT: B 151 CYS cc_start: 0.7582 (p) cc_final: 0.7380 (p) REVERT: B 199 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7586 (mm) REVERT: B 411 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7716 (tt) outliers start: 23 outliers final: 13 residues processed: 83 average time/residue: 1.0550 time to fit residues: 96.6517 Evaluate side-chains 85 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117368 restraints weight = 19437.291| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.27 r_work: 0.3201 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8861 Z= 0.283 Angle : 0.564 7.774 12119 Z= 0.289 Chirality : 0.042 0.164 1418 Planarity : 0.004 0.037 1466 Dihedral : 8.680 57.520 1416 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.75 % Allowed : 13.73 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1078 helix: 1.97 (0.22), residues: 531 sheet: -0.54 (0.47), residues: 123 loop : -1.57 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 PHE 0.016 0.001 PHE A 601 TYR 0.018 0.001 TYR B 570 ARG 0.005 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.975 Fit side-chains REVERT: A 78 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7766 (mmtt) REVERT: A 135 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7918 (p90) REVERT: A 180 ASP cc_start: 0.7456 (t0) cc_final: 0.6620 (p0) REVERT: A 337 ARG cc_start: 0.7751 (tmt170) cc_final: 0.7337 (ttt-90) REVERT: A 370 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8071 (mttp) REVERT: A 477 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: A 481 TYR cc_start: 0.8868 (t80) cc_final: 0.8625 (t80) REVERT: A 605 MET cc_start: 0.8596 (mmm) cc_final: 0.8309 (mpp) REVERT: B 199 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7486 (mm) REVERT: B 411 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7696 (tt) outliers start: 24 outliers final: 12 residues processed: 81 average time/residue: 0.9686 time to fit residues: 85.9546 Evaluate side-chains 81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.142022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113189 restraints weight = 14046.172| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.77 r_work: 0.3155 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8861 Z= 0.316 Angle : 0.577 8.026 12119 Z= 0.296 Chirality : 0.043 0.168 1418 Planarity : 0.004 0.037 1466 Dihedral : 8.610 57.597 1416 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 2.75 % Allowed : 13.84 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1078 helix: 1.90 (0.22), residues: 531 sheet: -0.56 (0.47), residues: 123 loop : -1.59 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 PHE 0.016 0.001 PHE B 601 TYR 0.018 0.002 TYR B 570 ARG 0.006 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.870 Fit side-chains REVERT: A 78 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7718 (mmtt) REVERT: A 135 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7926 (p90) REVERT: A 180 ASP cc_start: 0.7390 (t0) cc_final: 0.6614 (p0) REVERT: A 337 ARG cc_start: 0.7711 (tmt170) cc_final: 0.7434 (ttt-90) REVERT: A 370 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8001 (mttp) REVERT: A 477 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7814 (m-30) REVERT: A 605 MET cc_start: 0.8554 (mmm) cc_final: 0.8259 (mpp) REVERT: B 199 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7569 (mm) REVERT: B 411 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7667 (tt) outliers start: 24 outliers final: 14 residues processed: 82 average time/residue: 0.9138 time to fit residues: 82.0941 Evaluate side-chains 83 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 97 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS B 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.118504 restraints weight = 18671.104| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.02 r_work: 0.3222 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8861 Z= 0.248 Angle : 0.550 8.263 12119 Z= 0.282 Chirality : 0.041 0.158 1418 Planarity : 0.003 0.035 1466 Dihedral : 8.300 57.964 1416 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 2.29 % Allowed : 14.53 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1078 helix: 2.01 (0.22), residues: 531 sheet: -0.53 (0.47), residues: 123 loop : -1.56 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.016 0.001 PHE A 601 TYR 0.017 0.001 TYR B 570 ARG 0.006 0.000 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.823 Fit side-chains REVERT: A 78 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7718 (mmtt) REVERT: A 135 HIS cc_start: 0.8257 (OUTLIER) cc_final: 0.7950 (p90) REVERT: A 180 ASP cc_start: 0.7421 (t0) cc_final: 0.6630 (p0) REVERT: A 337 ARG cc_start: 0.7707 (tmt170) cc_final: 0.7294 (ttt-90) REVERT: A 370 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8046 (mttp) REVERT: A 477 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: A 481 TYR cc_start: 0.8834 (t80) cc_final: 0.8634 (t80) REVERT: A 533 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8277 (mt) REVERT: B 199 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7495 (mm) REVERT: B 411 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7648 (tt) outliers start: 20 outliers final: 12 residues processed: 80 average time/residue: 0.9206 time to fit residues: 80.6314 Evaluate side-chains 83 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118689 restraints weight = 18652.984| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.11 r_work: 0.3221 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8861 Z= 0.247 Angle : 0.551 8.458 12119 Z= 0.282 Chirality : 0.041 0.159 1418 Planarity : 0.004 0.058 1466 Dihedral : 8.134 55.068 1416 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.52 % Allowed : 14.65 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1078 helix: 2.12 (0.22), residues: 525 sheet: -0.46 (0.47), residues: 121 loop : -1.60 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.018 0.001 PHE A 601 TYR 0.017 0.001 TYR B 570 ARG 0.004 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.852 Fit side-chains REVERT: A 78 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7736 (mmtt) REVERT: A 135 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7933 (p90) REVERT: A 180 ASP cc_start: 0.7444 (t0) cc_final: 0.6629 (p0) REVERT: A 337 ARG cc_start: 0.7723 (tmt170) cc_final: 0.7300 (ttt-90) REVERT: A 370 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8074 (mttp) REVERT: A 477 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 481 TYR cc_start: 0.8856 (t80) cc_final: 0.8630 (t80) REVERT: B 199 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7536 (mm) REVERT: B 411 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7666 (tt) outliers start: 22 outliers final: 12 residues processed: 80 average time/residue: 0.9393 time to fit residues: 82.2861 Evaluate side-chains 82 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.146471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116487 restraints weight = 21047.345| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.11 r_work: 0.3201 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8861 Z= 0.307 Angle : 0.578 8.591 12119 Z= 0.296 Chirality : 0.042 0.166 1418 Planarity : 0.004 0.055 1466 Dihedral : 8.269 57.784 1416 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.56 % Favored : 95.35 % Rotamer: Outliers : 2.40 % Allowed : 14.53 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1078 helix: 2.01 (0.22), residues: 525 sheet: -0.51 (0.47), residues: 123 loop : -1.55 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 PHE 0.016 0.001 PHE B 601 TYR 0.018 0.002 TYR B 570 ARG 0.004 0.000 ARG A 412 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.905 Fit side-chains REVERT: A 78 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7557 (mmtt) REVERT: A 135 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.7926 (p90) REVERT: A 180 ASP cc_start: 0.7441 (t0) cc_final: 0.6513 (p0) REVERT: A 337 ARG cc_start: 0.7622 (tmt170) cc_final: 0.7149 (ttt-90) REVERT: A 370 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7991 (mttp) REVERT: A 477 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7651 (m-30) REVERT: A 527 ARG cc_start: 0.6036 (ptt-90) cc_final: 0.5679 (pmt170) REVERT: B 199 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7393 (mm) REVERT: B 411 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7481 (tt) outliers start: 21 outliers final: 12 residues processed: 78 average time/residue: 0.9549 time to fit residues: 81.6775 Evaluate side-chains 80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 614 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119502 restraints weight = 15132.924| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.17 r_work: 0.3228 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8861 Z= 0.259 Angle : 0.560 8.542 12119 Z= 0.287 Chirality : 0.042 0.161 1418 Planarity : 0.004 0.057 1466 Dihedral : 8.170 56.637 1416 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.17 % Allowed : 14.87 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1078 helix: 2.09 (0.22), residues: 525 sheet: -0.43 (0.47), residues: 121 loop : -1.60 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.016 0.001 PHE A 601 TYR 0.018 0.001 TYR B 570 ARG 0.004 0.000 ARG A 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5583.53 seconds wall clock time: 99 minutes 52.39 seconds (5992.39 seconds total)