Starting phenix.real_space_refine on Wed Sep 17 12:24:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vkj_43319/09_2025/8vkj_43319.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vkj_43319/09_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_43319/09_2025/8vkj_43319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vkj_43319/09_2025/8vkj_43319.map" model { file = "/net/cci-nas-00/data/ceres_data/8vkj_43319/09_2025/8vkj_43319.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vkj_43319/09_2025/8vkj_43319.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} 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: {'GLU:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} 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: {'GLU:plan': 4, 'ASP:plan': 3, 'ASN:plan1': 3, 'ARG:plan': 2, 'PHE:plan': 1, 'TRP:plan': 1} 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: 3.25, per 1000 atoms: 0.38 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: 0.88 Conformation dependent library (CDL) restraints added in 499.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.25 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: 1.53 Time building geometry restraints manager: 1.14 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 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 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: 8.010 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.370 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.000 ------------------------------------------------------------------------------- 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 8874 Z= 0.196 Angle : 0.641 19.887 12152 Z= 0.333 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 412 TYR 0.014 0.001 TYR B 570 PHE 0.014 0.001 PHE B 322 TRP 0.016 0.001 TRP A 418 HIS 0.004 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8861) covalent geometry : angle 0.62716 (12119) SS BOND : bond 0.00467 ( 6) SS BOND : angle 1.24112 ( 12) hydrogen bonds : bond 0.14337 ( 499) hydrogen bonds : angle 6.12165 ( 1446) link_BETA1-4 : bond 0.02316 ( 1) link_BETA1-4 : angle 5.21611 ( 3) link_NAG-ASN : bond 0.00528 ( 6) link_NAG-ASN : angle 2.69712 ( 18) *********************** 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 : 0.407 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 0.6122 time to fit residues: 40.7645 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 : 0.316 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.142753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111985 restraints weight = 19504.877| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.15 r_work: 0.3134 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 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 = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.0625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8874 Z= 0.204 Angle : 0.615 10.340 12152 Z= 0.312 Chirality : 0.043 0.162 1418 Planarity : 0.005 0.078 1466 Dihedral : 10.098 75.552 1417 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.06 % Allowed : 10.30 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.26), residues: 1078 helix: 1.92 (0.22), residues: 529 sheet: -0.22 (0.50), residues: 122 loop : -1.60 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 527 TYR 0.017 0.002 TYR B 570 PHE 0.016 0.001 PHE B 601 TRP 0.011 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 8861) covalent geometry : angle 0.60097 (12119) SS BOND : bond 0.00626 ( 6) SS BOND : angle 1.19712 ( 12) hydrogen bonds : bond 0.04270 ( 499) hydrogen bonds : angle 5.05954 ( 1446) link_BETA1-4 : bond 0.01392 ( 1) link_BETA1-4 : angle 3.52844 ( 3) link_NAG-ASN : bond 0.00567 ( 6) link_NAG-ASN : angle 2.97029 ( 18) *********************** 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: 18 poor density : 71 time to evaluate : 0.492 Fit side-chains REVERT: A 78 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7659 (mmtt) REVERT: A 180 ASP cc_start: 0.7430 (t0) cc_final: 0.6662 (p0) outliers start: 18 outliers final: 9 residues processed: 80 average time/residue: 0.5025 time to fit residues: 43.6283 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 : 0.341 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 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 516 GLN B 87 HIS B 140 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111710 restraints weight = 24272.957| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.39 r_work: 0.3116 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 8874 Z= 0.182 Angle : 0.583 9.898 12152 Z= 0.296 Chirality : 0.042 0.162 1418 Planarity : 0.004 0.037 1466 Dihedral : 9.418 64.876 1416 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.86 % Allowed : 11.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.26), residues: 1078 helix: 1.94 (0.22), residues: 531 sheet: -0.41 (0.48), residues: 122 loop : -1.55 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 412 TYR 0.017 0.001 TYR B 570 PHE 0.016 0.001 PHE B 601 TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8861) covalent geometry : angle 0.56993 (12119) SS BOND : bond 0.00510 ( 6) SS BOND : angle 1.04890 ( 12) hydrogen bonds : bond 0.03923 ( 499) hydrogen bonds : angle 4.84864 ( 1446) link_BETA1-4 : bond 0.00929 ( 1) link_BETA1-4 : angle 3.37804 ( 3) link_NAG-ASN : bond 0.00516 ( 6) link_NAG-ASN : angle 2.86405 ( 18) *********************** 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 95 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 70 time to evaluate : 0.387 Fit side-chains REVERT: A 78 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7688 (mmtt) REVERT: A 135 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.7818 (p90) REVERT: A 180 ASP cc_start: 0.7442 (t0) cc_final: 0.6682 (p0) REVERT: A 337 ARG cc_start: 0.7826 (tmt170) cc_final: 0.7495 (ttt-90) REVERT: B 151 CYS cc_start: 0.7683 (p) cc_final: 0.7463 (p) REVERT: B 199 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7524 (mm) REVERT: B 411 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7697 (tt) outliers start: 25 outliers final: 9 residues processed: 87 average time/residue: 0.4751 time to fit residues: 45.0010 Evaluate side-chains 82 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 37 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 79 optimal weight: 0.0040 chunk 74 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.147394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118073 restraints weight = 19250.465| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.12 r_work: 0.3216 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8874 Z= 0.169 Angle : 0.571 9.914 12152 Z= 0.289 Chirality : 0.042 0.160 1418 Planarity : 0.004 0.037 1466 Dihedral : 9.124 59.651 1416 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 2.52 % Allowed : 12.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.26), residues: 1078 helix: 2.02 (0.22), residues: 531 sheet: -0.51 (0.47), residues: 122 loop : -1.56 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.017 0.001 TYR B 570 PHE 0.016 0.001 PHE B 601 TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8861) covalent geometry : angle 0.55916 (12119) SS BOND : bond 0.00497 ( 6) SS BOND : angle 0.99030 ( 12) hydrogen bonds : bond 0.03735 ( 499) hydrogen bonds : angle 4.73635 ( 1446) link_BETA1-4 : bond 0.00790 ( 1) link_BETA1-4 : angle 2.80554 ( 3) link_NAG-ASN : bond 0.00538 ( 6) link_NAG-ASN : angle 2.82948 ( 18) *********************** 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 88 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.297 Fit side-chains REVERT: A 78 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7751 (mmtt) REVERT: A 135 HIS cc_start: 0.8272 (OUTLIER) cc_final: 0.7879 (p90) REVERT: A 180 ASP cc_start: 0.7414 (t0) cc_final: 0.6684 (p0) REVERT: A 337 ARG cc_start: 0.7796 (tmt170) cc_final: 0.7396 (ttt-90) REVERT: B 199 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7611 (mm) REVERT: B 411 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7708 (tt) outliers start: 22 outliers final: 10 residues processed: 79 average time/residue: 0.4797 time to fit residues: 41.2006 Evaluate side-chains 78 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 87 optimal weight: 0.0370 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.0000 overall best weight: 0.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 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 = 0.3658 r_free = 0.3658 target = 0.145617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.115392 restraints weight = 19667.650| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.29 r_work: 0.3166 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8874 Z= 0.131 Angle : 0.536 9.345 12152 Z= 0.272 Chirality : 0.041 0.150 1418 Planarity : 0.003 0.032 1466 Dihedral : 8.595 59.546 1416 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 2.17 % Allowed : 13.39 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.26), residues: 1078 helix: 2.09 (0.22), residues: 537 sheet: -0.47 (0.46), residues: 122 loop : -1.47 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.016 0.001 TYR B 570 PHE 0.016 0.001 PHE A 601 TRP 0.011 0.001 TRP A 647 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8861) covalent geometry : angle 0.52437 (12119) SS BOND : bond 0.00400 ( 6) SS BOND : angle 0.88623 ( 12) hydrogen bonds : bond 0.03517 ( 499) hydrogen bonds : angle 4.55010 ( 1446) link_BETA1-4 : bond 0.00703 ( 1) link_BETA1-4 : angle 2.45401 ( 3) link_NAG-ASN : bond 0.00526 ( 6) link_NAG-ASN : angle 2.66123 ( 18) *********************** 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 88 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.341 Fit side-chains REVERT: A 135 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7861 (p90) REVERT: A 180 ASP cc_start: 0.7355 (t0) cc_final: 0.6564 (p0) REVERT: A 337 ARG cc_start: 0.7717 (tmt170) cc_final: 0.7279 (ttt-90) REVERT: A 370 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7991 (mttp) REVERT: B 199 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7520 (mm) REVERT: B 411 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7599 (tt) outliers start: 19 outliers final: 10 residues processed: 81 average time/residue: 0.4623 time to fit residues: 40.9199 Evaluate side-chains 78 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 370 LYS 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 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 B 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.146275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117725 restraints weight = 23354.994| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.31 r_work: 0.3214 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 8874 Z= 0.207 Angle : 0.592 9.684 12152 Z= 0.300 Chirality : 0.043 0.171 1418 Planarity : 0.004 0.038 1466 Dihedral : 8.618 59.173 1416 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.47 % Favored : 95.44 % Rotamer: Outliers : 2.52 % Allowed : 13.62 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.25), residues: 1078 helix: 1.94 (0.22), residues: 537 sheet: -0.53 (0.46), residues: 123 loop : -1.54 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 412 TYR 0.018 0.002 TYR B 570 PHE 0.018 0.002 PHE A 601 TRP 0.012 0.001 TRP B 647 HIS 0.006 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 8861) covalent geometry : angle 0.58078 (12119) SS BOND : bond 0.00615 ( 6) SS BOND : angle 1.20987 ( 12) hydrogen bonds : bond 0.03787 ( 499) hydrogen bonds : angle 4.71865 ( 1446) link_BETA1-4 : bond 0.00819 ( 1) link_BETA1-4 : angle 2.27179 ( 3) link_NAG-ASN : bond 0.00514 ( 6) link_NAG-ASN : angle 2.80338 ( 18) *********************** 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 88 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.335 Fit side-chains REVERT: A 78 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7720 (mmtt) REVERT: A 180 ASP cc_start: 0.7447 (t0) cc_final: 0.6598 (p0) REVERT: A 337 ARG cc_start: 0.7721 (tmt170) cc_final: 0.7291 (ttt-90) REVERT: A 370 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8066 (mttp) REVERT: B 199 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7479 (mm) REVERT: B 411 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7643 (tt) outliers start: 22 outliers final: 12 residues processed: 80 average time/residue: 0.4781 time to fit residues: 41.6623 Evaluate side-chains 80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 370 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 54 optimal weight: 0.0370 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3653 r_free = 0.3653 target = 0.145023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114874 restraints weight = 19039.190| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.29 r_work: 0.3159 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.003 0.059 8874 Z= 0.141 Angle : 0.541 9.381 12152 Z= 0.275 Chirality : 0.041 0.153 1418 Planarity : 0.003 0.032 1466 Dihedral : 8.144 55.806 1416 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 2.40 % Allowed : 13.96 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.26), residues: 1078 helix: 2.13 (0.22), residues: 531 sheet: -0.41 (0.46), residues: 122 loop : -1.53 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.016 0.001 TYR B 570 PHE 0.015 0.001 PHE B 601 TRP 0.011 0.001 TRP A 647 HIS 0.004 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8861) covalent geometry : angle 0.52988 (12119) SS BOND : bond 0.00431 ( 6) SS BOND : angle 0.99514 ( 12) hydrogen bonds : bond 0.03538 ( 499) hydrogen bonds : angle 4.53170 ( 1446) link_BETA1-4 : bond 0.00745 ( 1) link_BETA1-4 : angle 2.12202 ( 3) link_NAG-ASN : bond 0.00520 ( 6) link_NAG-ASN : angle 2.69295 ( 18) *********************** 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 88 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.392 Fit side-chains REVERT: A 180 ASP cc_start: 0.7428 (t0) cc_final: 0.6587 (p0) REVERT: A 337 ARG cc_start: 0.7658 (tmt170) cc_final: 0.7241 (ttt-90) REVERT: A 370 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7991 (mttp) REVERT: A 481 TYR cc_start: 0.8793 (t80) cc_final: 0.8574 (t80) REVERT: B 199 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7416 (mm) REVERT: B 411 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7596 (tt) outliers start: 21 outliers final: 11 residues processed: 82 average time/residue: 0.4639 time to fit residues: 41.5947 Evaluate side-chains 81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 370 LYS 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 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 355 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 0.0870 chunk 32 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.144197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115951 restraints weight = 14688.474| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.12 r_work: 0.3170 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8874 Z= 0.163 Angle : 0.562 9.410 12152 Z= 0.285 Chirality : 0.041 0.160 1418 Planarity : 0.003 0.035 1466 Dihedral : 8.061 55.343 1416 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 1.95 % Allowed : 14.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1078 helix: 2.06 (0.22), residues: 537 sheet: -0.44 (0.47), residues: 123 loop : -1.51 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.017 0.001 TYR B 570 PHE 0.017 0.001 PHE A 601 TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8861) covalent geometry : angle 0.55114 (12119) SS BOND : bond 0.00499 ( 6) SS BOND : angle 1.07273 ( 12) hydrogen bonds : bond 0.03653 ( 499) hydrogen bonds : angle 4.57598 ( 1446) link_BETA1-4 : bond 0.00722 ( 1) link_BETA1-4 : angle 1.95226 ( 3) link_NAG-ASN : bond 0.00508 ( 6) link_NAG-ASN : angle 2.70465 ( 18) *********************** 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 82 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.371 Fit side-chains REVERT: A 135 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7956 (p90) REVERT: A 180 ASP cc_start: 0.7349 (t0) cc_final: 0.6538 (p0) REVERT: A 337 ARG cc_start: 0.7634 (tmt170) cc_final: 0.7218 (ttt-90) REVERT: A 370 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7989 (mttp) REVERT: A 481 TYR cc_start: 0.8784 (t80) cc_final: 0.8576 (t80) REVERT: B 199 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7527 (mm) REVERT: B 411 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7563 (tt) outliers start: 17 outliers final: 11 residues processed: 76 average time/residue: 0.4668 time to fit residues: 38.8189 Evaluate side-chains 81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 106 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 29 optimal weight: 0.0010 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.144586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116936 restraints weight = 13350.068| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.01 r_work: 0.3179 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8874 Z= 0.158 Angle : 0.560 9.389 12152 Z= 0.284 Chirality : 0.041 0.159 1418 Planarity : 0.004 0.053 1466 Dihedral : 7.974 55.118 1416 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 2.29 % Allowed : 14.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.26), residues: 1078 helix: 2.11 (0.22), residues: 531 sheet: -0.42 (0.46), residues: 123 loop : -1.59 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 412 TYR 0.017 0.001 TYR B 570 PHE 0.016 0.001 PHE A 601 TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8861) covalent geometry : angle 0.54894 (12119) SS BOND : bond 0.00487 ( 6) SS BOND : angle 1.07136 ( 12) hydrogen bonds : bond 0.03623 ( 499) hydrogen bonds : angle 4.56173 ( 1446) link_BETA1-4 : bond 0.00702 ( 1) link_BETA1-4 : angle 1.82774 ( 3) link_NAG-ASN : bond 0.00504 ( 6) link_NAG-ASN : angle 2.69406 ( 18) *********************** 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 85 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.342 Fit side-chains REVERT: A 78 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7616 (mmtt) REVERT: A 135 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7944 (p90) REVERT: A 180 ASP cc_start: 0.7365 (t0) cc_final: 0.6543 (p0) REVERT: A 337 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7231 (ttt-90) REVERT: A 370 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7979 (mttp) REVERT: A 481 TYR cc_start: 0.8776 (t80) cc_final: 0.8549 (t80) REVERT: A 527 ARG cc_start: 0.5987 (ptt-90) cc_final: 0.5598 (pmt170) REVERT: B 199 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7502 (mm) REVERT: B 411 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7555 (tt) outliers start: 20 outliers final: 12 residues processed: 80 average time/residue: 0.4728 time to fit residues: 41.2751 Evaluate side-chains 81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 355 ILE 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 48 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3645 r_free = 0.3645 target = 0.144166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113841 restraints weight = 19668.896| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.26 r_work: 0.3143 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 8874 Z= 0.164 Angle : 0.565 9.410 12152 Z= 0.287 Chirality : 0.041 0.160 1418 Planarity : 0.004 0.053 1466 Dihedral : 7.970 54.832 1416 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.19 % Favored : 95.72 % Rotamer: Outliers : 1.83 % Allowed : 15.45 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1078 helix: 2.08 (0.22), residues: 531 sheet: -0.41 (0.46), residues: 117 loop : -1.64 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 412 TYR 0.017 0.001 TYR B 570 PHE 0.016 0.001 PHE A 601 TRP 0.012 0.001 TRP B 647 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8861) covalent geometry : angle 0.55458 (12119) SS BOND : bond 0.00505 ( 6) SS BOND : angle 1.10718 ( 12) hydrogen bonds : bond 0.03662 ( 499) hydrogen bonds : angle 4.57265 ( 1446) link_BETA1-4 : bond 0.00677 ( 1) link_BETA1-4 : angle 1.74353 ( 3) link_NAG-ASN : bond 0.00503 ( 6) link_NAG-ASN : angle 2.70131 ( 18) ********************** 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 81 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.253 Fit side-chains REVERT: A 78 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7661 (mmtt) REVERT: A 135 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7958 (p90) REVERT: A 180 ASP cc_start: 0.7409 (t0) cc_final: 0.6587 (p0) REVERT: A 337 ARG cc_start: 0.7690 (tmt170) cc_final: 0.7266 (ttt-90) REVERT: A 370 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8016 (mttp) REVERT: B 199 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7460 (mm) REVERT: B 411 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7578 (tt) outliers start: 16 outliers final: 12 residues processed: 77 average time/residue: 0.4634 time to fit residues: 38.7213 Evaluate side-chains 82 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 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 199 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 355 ILE 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 34 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 35 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 54 optimal weight: 0.0470 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.146211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.115657 restraints weight = 19814.250| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.34 r_work: 0.3163 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8874 Z= 0.132 Angle : 0.540 9.125 12152 Z= 0.274 Chirality : 0.040 0.152 1418 Planarity : 0.003 0.046 1466 Dihedral : 7.699 54.888 1416 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 1.95 % Allowed : 15.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.26), residues: 1078 helix: 2.29 (0.22), residues: 525 sheet: -0.25 (0.47), residues: 115 loop : -1.58 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 412 TYR 0.016 0.001 TYR B 570 PHE 0.016 0.001 PHE A 601 TRP 0.011 0.001 TRP A 647 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8861) covalent geometry : angle 0.52978 (12119) SS BOND : bond 0.00406 ( 6) SS BOND : angle 0.93886 ( 12) hydrogen bonds : bond 0.03502 ( 499) hydrogen bonds : angle 4.45599 ( 1446) link_BETA1-4 : bond 0.00717 ( 1) link_BETA1-4 : angle 1.72211 ( 3) link_NAG-ASN : bond 0.00498 ( 6) link_NAG-ASN : angle 2.59127 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3066.56 seconds wall clock time: 53 minutes 13.88 seconds (3193.88 seconds total)