Starting phenix.real_space_refine on Thu Jul 2 21:13:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rx3_24723/07_2026/7rx3_24723.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rx3_24723/07_2026/7rx3_24723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rx3_24723/07_2026/7rx3_24723.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rx3_24723/07_2026/7rx3_24723.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rx3_24723/07_2026/7rx3_24723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rx3_24723/07_2026/7rx3_24723.map" model { file = "/net/cci-nas-00/data/ceres_data/7rx3_24723/07_2026/7rx3_24723.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rx3_24723/07_2026/7rx3_24723.cif" } resolution = 3.3 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 38 5.16 5 C 6684 2.51 5 N 1600 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10130 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4786 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 4786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4786 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 279 Unusual residues: {'PGW': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 279 Unusual residues: {'PGW': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PGW:plan-3': 4} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 2.28, per 1000 atoms: 0.23 Number of scatterers: 10130 At special positions: 0 Unit cell: (128.26, 96.46, 101.76, 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 38 16.00 P 14 15.00 O 1794 8.00 N 1600 7.00 C 6684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 331.0 milliseconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 72.3% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 28 through 46 removed outlier: 3.977A pdb=" N ALA B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 34 " --> pdb=" O PRO B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 87 Processing helix chain 'B' and resid 104 through 117 removed outlier: 3.997A pdb=" N ILE B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.832A pdb=" N TRP B 155 " --> pdb=" O CYS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.789A pdb=" N THR B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 204 removed outlier: 3.741A pdb=" N TYR B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix removed outlier: 3.678A pdb=" N TRP B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.878A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.512A pdb=" N ARG B 276 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 311 removed outlier: 3.575A pdb=" N PHE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 322 through 350 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 354 through 375 Processing helix chain 'B' and resid 375 through 383 removed outlier: 4.040A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 422 through 435 removed outlier: 4.084A pdb=" N LEU B 426 " --> pdb=" O ASN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.820A pdb=" N GLY B 441 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 501 removed outlier: 3.605A pdb=" N THR B 495 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 524 removed outlier: 4.567A pdb=" N GLU B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET B 515 " --> pdb=" O ASP B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.667A pdb=" N ASN B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 554 Processing helix chain 'B' and resid 568 through 592 removed outlier: 3.677A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 589 " --> pdb=" O SER B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 633 removed outlier: 4.078A pdb=" N LEU B 612 " --> pdb=" O TRP B 608 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 623 " --> pdb=" O HIS B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 659 removed outlier: 3.948A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 658 " --> pdb=" O TYR B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 removed outlier: 4.120A pdb=" N MET B 707 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG B 708 " --> pdb=" O PHE B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 708' Processing helix chain 'B' and resid 712 through 727 Processing helix chain 'A' and resid 28 through 46 removed outlier: 3.977A pdb=" N ALA A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 87 Processing helix chain 'A' and resid 104 through 117 removed outlier: 3.997A pdb=" N ILE A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.833A pdb=" N TRP A 155 " --> pdb=" O CYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.789A pdb=" N THR A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 204 removed outlier: 3.741A pdb=" N TYR A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix removed outlier: 3.678A pdb=" N TRP A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.879A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 280 removed outlier: 3.512A pdb=" N ARG A 276 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 311 removed outlier: 3.575A pdb=" N PHE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 322 Processing helix chain 'A' and resid 322 through 350 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 375 through 383 removed outlier: 4.041A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 422 through 435 removed outlier: 4.084A pdb=" N LEU A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.821A pdb=" N GLY A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 501 removed outlier: 3.605A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 524 removed outlier: 4.567A pdb=" N GLU A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 515 " --> pdb=" O ASP A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.668A pdb=" N ASN A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'A' and resid 568 through 592 removed outlier: 3.676A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 633 removed outlier: 4.078A pdb=" N LEU A 612 " --> pdb=" O TRP A 608 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 623 " --> pdb=" O HIS A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 659 removed outlier: 3.948A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 658 " --> pdb=" O TYR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 4.120A pdb=" N MET A 707 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG A 708 " --> pdb=" O PHE A 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 704 through 708' Processing helix chain 'A' and resid 712 through 727 Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 54 removed outlier: 3.756A pdb=" N ARG B 53 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B 61 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 22 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL B 19 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ILE B 139 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARG B 21 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 256 through 257 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 54 removed outlier: 3.756A pdb=" N ARG A 53 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 61 " --> pdb=" O ARG A 53 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 22 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 19 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ILE A 139 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARG A 21 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 257 590 hydrogen bonds defined for protein. 1752 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: 1.59 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1512 1.30 - 1.43: 2940 1.43 - 1.56: 5818 1.56 - 1.69: 34 1.69 - 1.82: 56 Bond restraints: 10360 Sorted by residual: bond pdb=" C1 PGW B 807 " pdb=" O01 PGW B 807 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1 PGW A 902 " pdb=" O01 PGW A 902 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C1 PGW B 803 " pdb=" O01 PGW B 803 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 PGW A 906 " pdb=" O01 PGW A 906 " ideal model delta sigma weight residual 1.332 1.424 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C1 PGW A 901 " pdb=" O01 PGW A 901 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 10355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 13028 2.35 - 4.70: 662 4.70 - 7.05: 178 7.05 - 9.40: 52 9.40 - 11.75: 34 Bond angle restraints: 13954 Sorted by residual: angle pdb=" C LYS B 158 " pdb=" N THR B 159 " pdb=" CA THR B 159 " ideal model delta sigma weight residual 121.54 132.59 -11.05 1.91e+00 2.74e-01 3.34e+01 angle pdb=" C LYS A 158 " pdb=" N THR A 159 " pdb=" CA THR A 159 " ideal model delta sigma weight residual 121.54 132.57 -11.03 1.91e+00 2.74e-01 3.33e+01 angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 112.96 107.84 5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" N VAL B 508 " pdb=" CA VAL B 508 " pdb=" C VAL B 508 " ideal model delta sigma weight residual 112.96 107.87 5.09 1.00e+00 1.00e+00 2.59e+01 angle pdb=" C LEU A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.24 123.42 -3.18 6.30e-01 2.52e+00 2.54e+01 ... (remaining 13949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.39: 5646 27.39 - 54.78: 394 54.78 - 82.17: 44 82.17 - 109.56: 18 109.56 - 136.96: 6 Dihedral angle restraints: 6108 sinusoidal: 2630 harmonic: 3478 Sorted by residual: dihedral pdb=" CA VAL B 117 " pdb=" C VAL B 117 " pdb=" N PRO B 118 " pdb=" CA PRO B 118 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL A 117 " pdb=" C VAL A 117 " pdb=" N PRO A 118 " pdb=" CA PRO A 118 " ideal model delta harmonic sigma weight residual -180.00 -153.46 -26.54 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" C08 PGW A 903 " pdb=" C06 PGW A 903 " pdb=" C07 PGW A 903 " pdb=" C10 PGW A 903 " ideal model delta sinusoidal sigma weight residual 178.64 -44.40 -136.96 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 6105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1003 0.049 - 0.098: 376 0.098 - 0.147: 104 0.147 - 0.197: 29 0.197 - 0.246: 10 Chirality restraints: 1522 Sorted by residual: chirality pdb=" C02 PGW B 806 " pdb=" C01 PGW B 806 " pdb=" C03 PGW B 806 " pdb=" O01 PGW B 806 " both_signs ideal model delta sigma weight residual False 2.36 2.60 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" C02 PGW A 901 " pdb=" C01 PGW A 901 " pdb=" C03 PGW A 901 " pdb=" O01 PGW A 901 " both_signs ideal model delta sigma weight residual False 2.36 2.60 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1519 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 317 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LYS A 317 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS A 317 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY A 318 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 317 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C LYS B 317 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 317 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY B 318 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 422 " -0.050 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO A 423 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 423 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 423 " -0.042 5.00e-02 4.00e+02 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3228 2.84 - 3.36: 8979 3.36 - 3.87: 16186 3.87 - 4.39: 18423 4.39 - 4.90: 32680 Nonbonded interactions: 79496 Sorted by model distance: nonbonded pdb=" O SER B 420 " pdb=" OG SER B 420 " model vdw 2.327 3.040 nonbonded pdb=" O SER A 420 " pdb=" OG SER A 420 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR A 589 " pdb=" O ILE A 605 " model vdw 2.350 3.040 nonbonded pdb=" OH TYR B 589 " pdb=" O ILE B 605 " model vdw 2.350 3.040 nonbonded pdb=" O SER A 207 " pdb=" OAE PGW A 905 " model vdw 2.359 3.040 ... (remaining 79491 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 901 or (resid 902 and (name C01 or name C02 or \ name C03 or name C15 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C \ 4 or name C5 or name O01 or name O02 or name O03 or name O04 or name O11)) or (r \ esid 903 and (name C01 or name C02 or name C03 or name C1 or name C19 or name C2 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C3 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name C9 or name O01 or name O02 or name O03 or name O04 or name O11 or nam \ e O12 or name O13 or name O14 or name P )) or (resid 904 and (name C01 or name C \ 02 or name C03 or name C06 or name C07 or name C08 or name C1 or name C10 or nam \ e C15 or name C16 or name C17 or name C19 or name C2 or name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or \ name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name O1 \ 4 or name P )) or resid 905 through 906 or (resid 907 and (name C01 or name C02 \ or name C03 or name C06 or name C1 or name C10 or name C15 or name C16 or name C \ 17 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or na \ me C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O03 or na \ me O04 or name O11)) or (resid 908 and (name C01 or name C02 or name C03 or name \ C1 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or na \ me C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or n \ ame C6 or name C7 or name O01 or name O02 or name O03 or name O04 or name O11 or \ name O12 or name O13 or name O14 or name P )))) selection = (chain 'B' and (resid 11 through 728 or (resid 801 and (name C01 or name C02 or \ name C03 or name C1 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C \ 25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name \ O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name O14 or n \ ame P )) or (resid 802 and (name C01 or name C02 or name C03 or name C15 or name \ C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or n \ ame C25 or name C26 or name C27 or name C3 or name C4 or name C5 or name O01 or \ name O02 or name O03 or name O04 or name O11)) or (resid 803 and (name C01 or na \ me C02 or name C03 or name C1 or name C19 or name C2 or name C20 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C3 \ or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name O01 or \ name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or name O1 \ 4 or name P )) or (resid 804 and (name C01 or name C02 or name C03 or name C06 o \ r name C07 or name C08 or name C1 or name C10 or name C15 or name C16 or name C1 \ 7 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name \ C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or nam \ e C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O03 or nam \ e O04 or name O11 or name O12 or name O13 or name O14 or name P )) or (resid 805 \ and (name C01 or name C02 or name C03 or name C04 or name C05 or name C1 or nam \ e C15 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or \ name C24 or name C25 or name C26 or name C27 or name C3 or name C4 or name C5 or \ name CAD or name O01 or name O02 or name O03 or name O04 or name O11 or name O1 \ 2 or name O13 or name O14 or name OAE or name OAF or name P )) or (resid 806 and \ (name C01 or name C02 or name C03 or name C1 or name C15 or name C19 or name C2 \ or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name \ C26 or name C27 or name C3 or name C4 or name C5 or name C6 or name C7 or name \ C8 or name C9 or name O01 or name O02 or name O03 or name O04 or name O11 or nam \ e O12 or name O13 or name O14 or name P )) or resid 807 or (resid 808 and (name \ C01 or name C02 or name C03 or name C1 or name C19 or name C2 or name C20 or nam \ e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ name C3 or name C4 or name C5 or name C6 or name C7 or name O01 or name O02 or \ name O03 or name O04 or name O11 or name O12 or name O13 or name O14 or name P ) \ ))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 1.610 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.200 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 : 0.009 0.092 10360 Z= 0.440 Angle : 1.375 11.750 13954 Z= 0.635 Chirality : 0.059 0.246 1522 Planarity : 0.008 0.076 1698 Dihedral : 18.794 136.955 3848 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.20 % Allowed : 8.27 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.19), residues: 1154 helix: -2.14 (0.13), residues: 800 sheet: -1.01 (0.71), residues: 44 loop : -3.82 (0.30), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 496 TYR 0.013 0.002 TYR A 24 PHE 0.016 0.002 PHE B 253 TRP 0.022 0.002 TRP A 155 HIS 0.005 0.002 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00929 / 0.44 (10360) covalent geometry : angle 1.37457 / 0.63 (13954) hydrogen bonds : bond 0.12409 / 8.40 ( 590) hydrogen bonds : angle 5.62740 / 3.87 ( 1752) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.318 Fit side-chains REVERT: B 84 TRP cc_start: 0.7073 (m100) cc_final: 0.5199 (t60) REVERT: B 442 PHE cc_start: 0.7746 (t80) cc_final: 0.7439 (t80) REVERT: A 84 TRP cc_start: 0.6945 (m100) cc_final: 0.5172 (t60) REVERT: A 442 PHE cc_start: 0.7706 (t80) cc_final: 0.7368 (t80) outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.0948 time to fit residues: 13.3659 Evaluate side-chains 58 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 GLN B 280 GLN B 283 GLN B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 GLN A 280 GLN A 283 GLN A 364 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109390 restraints weight = 13340.880| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.20 r_work: 0.3166 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10360 Z= 0.132 Angle : 0.585 7.457 13954 Z= 0.299 Chirality : 0.040 0.162 1522 Planarity : 0.005 0.056 1698 Dihedral : 16.163 108.171 1644 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.07 % Allowed : 10.24 % Favored : 87.70 % 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 are not related in a simple way. whole: -1.53 (0.24), residues: 1154 helix: -0.12 (0.18), residues: 806 sheet: -0.06 (0.66), residues: 44 loop : -3.48 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 250 TYR 0.013 0.001 TYR A 278 PHE 0.014 0.001 PHE B 61 TRP 0.011 0.001 TRP B 155 HIS 0.002 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (10360) covalent geometry : angle 0.58513 / 0.30 (13954) hydrogen bonds : bond 0.03745 / 2.59 ( 590) hydrogen bonds : angle 4.13772 / 2.85 ( 1752) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.379 Fit side-chains REVERT: B 84 TRP cc_start: 0.7018 (m100) cc_final: 0.4805 (t60) REVERT: B 277 MET cc_start: 0.7912 (ttp) cc_final: 0.7512 (mtp) REVERT: B 442 PHE cc_start: 0.7580 (t80) cc_final: 0.7221 (t80) REVERT: A 84 TRP cc_start: 0.7054 (m100) cc_final: 0.4796 (t60) REVERT: A 277 MET cc_start: 0.8004 (ttp) cc_final: 0.7787 (mtp) REVERT: A 442 PHE cc_start: 0.7543 (t80) cc_final: 0.7189 (t80) outliers start: 21 outliers final: 9 residues processed: 88 average time/residue: 0.0788 time to fit residues: 10.5369 Evaluate side-chains 69 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.0270 chunk 63 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109926 restraints weight = 13848.503| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.38 r_work: 0.3139 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10360 Z= 0.236 Angle : 0.649 8.240 13954 Z= 0.330 Chirality : 0.044 0.167 1522 Planarity : 0.005 0.067 1698 Dihedral : 15.240 116.069 1644 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.15 % Allowed : 12.11 % Favored : 84.74 % 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 are not related in a simple way. whole: -0.75 (0.25), residues: 1154 helix: 0.53 (0.19), residues: 796 sheet: -0.07 (0.67), residues: 44 loop : -3.26 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 149 TYR 0.014 0.002 TYR A 589 PHE 0.021 0.002 PHE B 61 TRP 0.019 0.002 TRP B 155 HIS 0.004 0.002 HIS A 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.24 (10360) covalent geometry : angle 0.64911 / 0.33 (13954) hydrogen bonds : bond 0.04405 / 3.03 ( 590) hydrogen bonds : angle 4.15477 / 2.85 ( 1752) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.365 Fit side-chains REVERT: B 84 TRP cc_start: 0.7168 (m100) cc_final: 0.4919 (t60) REVERT: B 442 PHE cc_start: 0.7632 (t80) cc_final: 0.7304 (t80) REVERT: A 84 TRP cc_start: 0.7148 (m100) cc_final: 0.4895 (t60) REVERT: A 442 PHE cc_start: 0.7612 (t80) cc_final: 0.7269 (t80) outliers start: 32 outliers final: 20 residues processed: 92 average time/residue: 0.0770 time to fit residues: 11.0341 Evaluate side-chains 81 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 712 TRP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 712 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 283 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106881 restraints weight = 13415.143| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.43 r_work: 0.3110 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10360 Z= 0.158 Angle : 0.585 9.021 13954 Z= 0.298 Chirality : 0.041 0.166 1522 Planarity : 0.005 0.054 1698 Dihedral : 14.142 110.332 1644 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.35 % Allowed : 13.48 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.26), residues: 1154 helix: 0.89 (0.19), residues: 800 sheet: -0.12 (0.66), residues: 44 loop : -3.32 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.009 0.001 TYR B 589 PHE 0.017 0.001 PHE B 61 TRP 0.020 0.002 TRP B 155 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (10360) covalent geometry : angle 0.58486 / 0.30 (13954) hydrogen bonds : bond 0.03679 / 2.52 ( 590) hydrogen bonds : angle 3.83422 / 2.65 ( 1752) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.311 Fit side-chains REVERT: B 84 TRP cc_start: 0.6935 (m100) cc_final: 0.4743 (t60) REVERT: B 442 PHE cc_start: 0.7515 (t80) cc_final: 0.7173 (t80) REVERT: A 84 TRP cc_start: 0.6921 (m100) cc_final: 0.4715 (t60) REVERT: A 442 PHE cc_start: 0.7490 (t80) cc_final: 0.7142 (t80) outliers start: 34 outliers final: 19 residues processed: 93 average time/residue: 0.0816 time to fit residues: 11.5418 Evaluate side-chains 80 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105576 restraints weight = 13429.716| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.23 r_work: 0.3112 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10360 Z= 0.203 Angle : 0.620 8.177 13954 Z= 0.315 Chirality : 0.043 0.165 1522 Planarity : 0.005 0.057 1698 Dihedral : 13.548 117.907 1644 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 3.74 % Allowed : 13.78 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.26), residues: 1154 helix: 0.96 (0.19), residues: 808 sheet: -0.26 (0.67), residues: 44 loop : -3.39 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 496 TYR 0.011 0.001 TYR B 589 PHE 0.020 0.002 PHE A 61 TRP 0.022 0.002 TRP B 155 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.20 (10360) covalent geometry : angle 0.62038 / 0.31 (13954) hydrogen bonds : bond 0.04054 / 2.79 ( 590) hydrogen bonds : angle 3.92734 / 2.71 ( 1752) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.364 Fit side-chains REVERT: B 84 TRP cc_start: 0.7032 (m100) cc_final: 0.4829 (t60) REVERT: B 442 PHE cc_start: 0.7593 (t80) cc_final: 0.7258 (t80) REVERT: A 84 TRP cc_start: 0.7030 (m100) cc_final: 0.4817 (t60) REVERT: A 442 PHE cc_start: 0.7590 (t80) cc_final: 0.7250 (t80) outliers start: 38 outliers final: 30 residues processed: 100 average time/residue: 0.0703 time to fit residues: 10.9279 Evaluate side-chains 95 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 712 TRP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 712 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 25 optimal weight: 7.9990 chunk 104 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108712 restraints weight = 13314.757| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.43 r_work: 0.3145 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10360 Z= 0.117 Angle : 0.546 7.584 13954 Z= 0.277 Chirality : 0.039 0.161 1522 Planarity : 0.005 0.055 1698 Dihedral : 12.612 103.360 1644 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 3.64 % Allowed : 15.16 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1154 helix: 1.24 (0.19), residues: 812 sheet: -0.21 (0.68), residues: 44 loop : -3.29 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.007 0.001 TYR A 18 PHE 0.015 0.001 PHE B 61 TRP 0.027 0.001 TRP A 155 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10360) covalent geometry : angle 0.54556 / 0.28 (13954) hydrogen bonds : bond 0.03323 / 2.28 ( 590) hydrogen bonds : angle 3.76428 / 2.59 ( 1752) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 67 time to evaluate : 0.370 Fit side-chains REVERT: B 84 TRP cc_start: 0.6811 (m100) cc_final: 0.4684 (t60) REVERT: B 442 PHE cc_start: 0.7516 (t80) cc_final: 0.7190 (t80) REVERT: A 84 TRP cc_start: 0.6779 (m100) cc_final: 0.4650 (t60) REVERT: A 442 PHE cc_start: 0.7523 (t80) cc_final: 0.7185 (t80) outliers start: 37 outliers final: 26 residues processed: 100 average time/residue: 0.0684 time to fit residues: 10.7693 Evaluate side-chains 86 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 92 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107488 restraints weight = 13337.154| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.24 r_work: 0.3151 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10360 Z= 0.140 Angle : 0.556 7.489 13954 Z= 0.282 Chirality : 0.040 0.159 1522 Planarity : 0.005 0.057 1698 Dihedral : 12.222 93.920 1644 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.94 % Allowed : 14.86 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.26), residues: 1154 helix: 1.31 (0.19), residues: 812 sheet: -0.10 (0.70), residues: 44 loop : -3.25 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 496 TYR 0.009 0.001 TYR A 589 PHE 0.016 0.001 PHE B 61 TRP 0.015 0.001 TRP A 155 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 (10360) covalent geometry : angle 0.55579 / 0.28 (13954) hydrogen bonds : bond 0.03447 / 2.36 ( 590) hydrogen bonds : angle 3.76223 / 2.59 ( 1752) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 66 time to evaluate : 0.359 Fit side-chains REVERT: B 84 TRP cc_start: 0.6811 (m100) cc_final: 0.4713 (t60) REVERT: B 442 PHE cc_start: 0.7585 (t80) cc_final: 0.7257 (t80) REVERT: A 84 TRP cc_start: 0.6837 (m100) cc_final: 0.4678 (t60) REVERT: A 442 PHE cc_start: 0.7578 (t80) cc_final: 0.7247 (t80) outliers start: 40 outliers final: 35 residues processed: 104 average time/residue: 0.0787 time to fit residues: 12.4082 Evaluate side-chains 95 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 75 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109620 restraints weight = 13314.372| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.22 r_work: 0.3165 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10360 Z= 0.123 Angle : 0.538 7.927 13954 Z= 0.274 Chirality : 0.039 0.158 1522 Planarity : 0.004 0.056 1698 Dihedral : 11.779 79.631 1644 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.94 % Allowed : 15.16 % Favored : 80.91 % 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 are not related in a simple way. whole: 0.36 (0.26), residues: 1154 helix: 1.43 (0.19), residues: 812 sheet: 0.04 (0.71), residues: 44 loop : -3.23 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 562 TYR 0.008 0.001 TYR B 589 PHE 0.014 0.001 PHE B 61 TRP 0.011 0.001 TRP B 227 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (10360) covalent geometry : angle 0.53789 / 0.27 (13954) hydrogen bonds : bond 0.03257 / 2.24 ( 590) hydrogen bonds : angle 3.70385 / 2.54 ( 1752) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 66 time to evaluate : 0.354 Fit side-chains REVERT: B 84 TRP cc_start: 0.6697 (m100) cc_final: 0.4664 (t60) REVERT: B 442 PHE cc_start: 0.7582 (t80) cc_final: 0.7259 (t80) REVERT: A 84 TRP cc_start: 0.6771 (m100) cc_final: 0.4671 (t60) REVERT: A 442 PHE cc_start: 0.7571 (t80) cc_final: 0.7246 (t80) outliers start: 40 outliers final: 31 residues processed: 102 average time/residue: 0.0638 time to fit residues: 10.1660 Evaluate side-chains 92 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 6 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.131550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.111461 restraints weight = 13369.697| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.21 r_work: 0.3146 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10360 Z= 0.134 Angle : 0.549 7.772 13954 Z= 0.278 Chirality : 0.040 0.158 1522 Planarity : 0.004 0.057 1698 Dihedral : 11.514 77.565 1644 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.35 % Allowed : 15.85 % Favored : 80.81 % 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 are not related in a simple way. whole: 0.41 (0.26), residues: 1154 helix: 1.48 (0.19), residues: 812 sheet: -0.01 (0.71), residues: 44 loop : -3.24 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.008 0.001 TYR B 589 PHE 0.015 0.001 PHE B 61 TRP 0.011 0.001 TRP B 202 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (10360) covalent geometry : angle 0.54864 / 0.28 (13954) hydrogen bonds : bond 0.03295 / 2.27 ( 590) hydrogen bonds : angle 3.69625 / 2.54 ( 1752) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.355 Fit side-chains REVERT: B 84 TRP cc_start: 0.6795 (m100) cc_final: 0.4791 (t60) REVERT: B 442 PHE cc_start: 0.7660 (t80) cc_final: 0.7344 (t80) REVERT: A 84 TRP cc_start: 0.6787 (m100) cc_final: 0.4755 (t60) REVERT: A 442 PHE cc_start: 0.7650 (t80) cc_final: 0.7336 (t80) outliers start: 34 outliers final: 31 residues processed: 95 average time/residue: 0.0631 time to fit residues: 9.5236 Evaluate side-chains 94 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 650 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 82 optimal weight: 0.2980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.110358 restraints weight = 13262.159| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.34 r_work: 0.3171 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10360 Z= 0.108 Angle : 0.525 7.368 13954 Z= 0.265 Chirality : 0.038 0.154 1522 Planarity : 0.004 0.056 1698 Dihedral : 10.679 71.692 1644 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.95 % Allowed : 16.54 % Favored : 80.51 % 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 are not related in a simple way. whole: 0.63 (0.27), residues: 1154 helix: 1.63 (0.19), residues: 814 sheet: 0.15 (0.70), residues: 44 loop : -3.19 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 562 TYR 0.006 0.001 TYR A 24 PHE 0.012 0.001 PHE B 61 TRP 0.012 0.001 TRP A 227 HIS 0.003 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10360) covalent geometry : angle 0.52501 / 0.27 (13954) hydrogen bonds : bond 0.02934 / 2.01 ( 590) hydrogen bonds : angle 3.56866 / 2.45 ( 1752) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 0.362 Fit side-chains REVERT: B 19 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8469 (t) REVERT: B 84 TRP cc_start: 0.6568 (m100) cc_final: 0.4667 (t60) REVERT: B 442 PHE cc_start: 0.7573 (t80) cc_final: 0.7262 (t80) REVERT: A 84 TRP cc_start: 0.6631 (m100) cc_final: 0.4662 (t60) REVERT: A 442 PHE cc_start: 0.7535 (t80) cc_final: 0.7212 (t80) outliers start: 30 outliers final: 28 residues processed: 99 average time/residue: 0.0641 time to fit residues: 9.7725 Evaluate side-chains 93 residues out of total 1048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 525 PHE Chi-restraints excluded: chain A residue 576 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 364 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.132567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110878 restraints weight = 13492.289| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.33 r_work: 0.3153 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10360 Z= 0.116 Angle : 0.533 7.265 13954 Z= 0.270 Chirality : 0.039 0.169 1522 Planarity : 0.005 0.070 1698 Dihedral : 10.576 72.674 1644 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.05 % Allowed : 16.63 % Favored : 80.31 % 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 are not related in a simple way. whole: 0.67 (0.27), residues: 1154 helix: 1.67 (0.19), residues: 816 sheet: 0.48 (0.71), residues: 44 loop : -3.26 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 562 TYR 0.007 0.001 TYR A 589 PHE 0.013 0.001 PHE B 61 TRP 0.011 0.001 TRP A 227 HIS 0.002 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (10360) covalent geometry : angle 0.53274 / 0.27 (13954) hydrogen bonds : bond 0.03031 / 2.09 ( 590) hydrogen bonds : angle 3.56545 / 2.45 ( 1752) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.93 seconds wall clock time: 35 minutes 51.47 seconds (2151.47 seconds total)