Starting phenix.real_space_refine on Wed Aug 5 17:52:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z4j_73805/08_2026/9z4j_73805_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z4j_73805/08_2026/9z4j_73805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z4j_73805/08_2026/9z4j_73805.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z4j_73805/08_2026/9z4j_73805.map" model { file = "/net/cci-nas-00/data/ceres_data/9z4j_73805/08_2026/9z4j_73805_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z4j_73805/08_2026/9z4j_73805_neut.cif" } resolution = 3.15 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= 0.001 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 Zn 1 6.06 5 S 54 5.16 5 C 7143 2.51 5 N 1704 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 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10699 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3565 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 4 Chain: "B" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3565 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 4 Chain: "C" Number of atoms: 3565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3565 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 20, 'TRANS': 440} Chain breaks: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.19 Number of scatterers: 10699 At special positions: 0 Unit cell: (120.596, 130.816, 76.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 3 19.99 S 54 16.00 O 1794 8.00 N 1704 7.00 C 7143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 259.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 581 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS B 581 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS C 581 " 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 80.5% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 82 through 90 removed outlier: 3.549A pdb=" N GLY A 86 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 122 removed outlier: 3.528A pdb=" N PHE A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 166 through 182 removed outlier: 3.915A pdb=" N ALA A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 198 through 223 Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.724A pdb=" N TRP A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.813A pdb=" N LEU A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 342 removed outlier: 4.019A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 374 removed outlier: 3.642A pdb=" N VAL A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 392 through 405 Processing helix chain 'A' and resid 418 through 452 removed outlier: 3.697A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 481 removed outlier: 4.277A pdb=" N ALA A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 515 removed outlier: 4.513A pdb=" N ILE A 496 " --> pdb=" O PHE A 492 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 546 Processing helix chain 'A' and resid 547 through 550 Processing helix chain 'A' and resid 554 through 577 removed outlier: 3.718A pdb=" N GLY A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 59 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.548A pdb=" N GLY B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 122 removed outlier: 3.527A pdb=" N PHE B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 166 through 182 removed outlier: 3.915A pdb=" N ALA B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 193 Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 227 through 251 removed outlier: 3.723A pdb=" N TRP B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.813A pdb=" N LEU B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 342 removed outlier: 4.019A pdb=" N LEU B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 374 removed outlier: 3.640A pdb=" N VAL B 364 " --> pdb=" O CYS B 360 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 392 through 405 Processing helix chain 'B' and resid 418 through 452 removed outlier: 3.697A pdb=" N ALA B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 423 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 481 removed outlier: 4.279A pdb=" N ALA B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 4.513A pdb=" N ILE B 496 " --> pdb=" O PHE B 492 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 497 " --> pdb=" O GLY B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 546 Processing helix chain 'B' and resid 547 through 550 Processing helix chain 'B' and resid 554 through 577 removed outlier: 3.717A pdb=" N GLY B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 59 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.548A pdb=" N GLY C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 122 removed outlier: 3.527A pdb=" N PHE C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 141 through 150 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 166 through 182 removed outlier: 3.915A pdb=" N ALA C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 Processing helix chain 'C' and resid 198 through 223 Processing helix chain 'C' and resid 227 through 251 removed outlier: 3.724A pdb=" N TRP C 249 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.812A pdb=" N LEU C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 342 removed outlier: 4.020A pdb=" N LEU C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 374 removed outlier: 3.641A pdb=" N VAL C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 392 through 405 Processing helix chain 'C' and resid 418 through 452 removed outlier: 3.697A pdb=" N ALA C 422 " --> pdb=" O HIS C 418 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 423 " --> pdb=" O TRP C 419 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 424 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 481 removed outlier: 4.278A pdb=" N ALA C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 515 removed outlier: 4.513A pdb=" N ILE C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 546 Processing helix chain 'C' and resid 547 through 550 Processing helix chain 'C' and resid 554 through 577 removed outlier: 3.718A pdb=" N GLY C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA5, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AA6, first strand: chain 'C' and resid 224 through 226 786 hydrogen bonds defined for protein. 2286 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: 1.58 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3164 1.34 - 1.46: 1896 1.46 - 1.58: 5836 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 10962 Sorted by residual: bond pdb=" C PHE B 577 " pdb=" N GLY B 578 " ideal model delta sigma weight residual 1.331 1.455 -0.124 1.29e-02 6.01e+03 9.22e+01 bond pdb=" C PHE A 577 " pdb=" N GLY A 578 " ideal model delta sigma weight residual 1.331 1.454 -0.123 1.29e-02 6.01e+03 9.13e+01 bond pdb=" C PHE C 577 " pdb=" N GLY C 578 " ideal model delta sigma weight residual 1.331 1.454 -0.123 1.29e-02 6.01e+03 9.07e+01 bond pdb=" CG HIS C 581 " pdb=" CD2 HIS C 581 " ideal model delta sigma weight residual 1.354 1.301 0.053 1.10e-02 8.26e+03 2.33e+01 bond pdb=" CG HIS A 581 " pdb=" CD2 HIS A 581 " ideal model delta sigma weight residual 1.354 1.301 0.053 1.10e-02 8.26e+03 2.32e+01 ... (remaining 10957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 14812 3.20 - 6.40: 140 6.40 - 9.59: 12 9.59 - 12.79: 3 12.79 - 15.99: 3 Bond angle restraints: 14970 Sorted by residual: angle pdb=" CA HIS B 581 " pdb=" CB HIS B 581 " pdb=" CG HIS B 581 " ideal model delta sigma weight residual 113.80 124.59 -10.79 1.00e+00 1.00e+00 1.16e+02 angle pdb=" CA HIS C 581 " pdb=" CB HIS C 581 " pdb=" CG HIS C 581 " ideal model delta sigma weight residual 113.80 124.58 -10.78 1.00e+00 1.00e+00 1.16e+02 angle pdb=" CA HIS A 581 " pdb=" CB HIS A 581 " pdb=" CG HIS A 581 " ideal model delta sigma weight residual 113.80 124.56 -10.76 1.00e+00 1.00e+00 1.16e+02 angle pdb=" C HIS C 581 " pdb=" CA HIS C 581 " pdb=" CB HIS C 581 " ideal model delta sigma weight residual 111.22 95.23 15.99 2.02e+00 2.45e-01 6.27e+01 angle pdb=" C HIS A 581 " pdb=" CA HIS A 581 " pdb=" CB HIS A 581 " ideal model delta sigma weight residual 111.22 95.23 15.99 2.02e+00 2.45e-01 6.26e+01 ... (remaining 14965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 5937 17.57 - 35.14: 285 35.14 - 52.70: 72 52.70 - 70.27: 12 70.27 - 87.84: 3 Dihedral angle restraints: 6309 sinusoidal: 2334 harmonic: 3975 Sorted by residual: dihedral pdb=" C HIS C 581 " pdb=" N HIS C 581 " pdb=" CA HIS C 581 " pdb=" CB HIS C 581 " ideal model delta harmonic sigma weight residual -122.60 -103.88 -18.72 0 2.50e+00 1.60e-01 5.61e+01 dihedral pdb=" C HIS A 581 " pdb=" N HIS A 581 " pdb=" CA HIS A 581 " pdb=" CB HIS A 581 " ideal model delta harmonic sigma weight residual -122.60 -103.92 -18.68 0 2.50e+00 1.60e-01 5.58e+01 dihedral pdb=" C HIS B 581 " pdb=" N HIS B 581 " pdb=" CA HIS B 581 " pdb=" CB HIS B 581 " ideal model delta harmonic sigma weight residual -122.60 -103.96 -18.64 0 2.50e+00 1.60e-01 5.56e+01 ... (remaining 6306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1702 0.082 - 0.165: 107 0.165 - 0.247: 12 0.247 - 0.330: 0 0.330 - 0.412: 3 Chirality restraints: 1824 Sorted by residual: chirality pdb=" CA HIS C 581 " pdb=" N HIS C 581 " pdb=" C HIS C 581 " pdb=" CB HIS C 581 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA HIS A 581 " pdb=" N HIS A 581 " pdb=" C HIS A 581 " pdb=" CB HIS A 581 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA HIS B 581 " pdb=" N HIS B 581 " pdb=" C HIS B 581 " pdb=" CB HIS B 581 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 1821 not shown) Planarity restraints: 1812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 581 " -0.055 2.00e-02 2.50e+03 4.67e-02 3.27e+01 pdb=" CG HIS C 581 " 0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS C 581 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS C 581 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 HIS C 581 " -0.063 2.00e-02 2.50e+03 pdb=" NE2 HIS C 581 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 581 " 0.055 2.00e-02 2.50e+03 4.65e-02 3.25e+01 pdb=" CG HIS B 581 " -0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS B 581 " -0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS B 581 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS B 581 " 0.063 2.00e-02 2.50e+03 pdb=" NE2 HIS B 581 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 581 " -0.055 2.00e-02 2.50e+03 4.64e-02 3.24e+01 pdb=" CG HIS A 581 " 0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS A 581 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 HIS A 581 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 581 " -0.063 2.00e-02 2.50e+03 pdb=" NE2 HIS A 581 " -0.011 2.00e-02 2.50e+03 ... (remaining 1809 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 481 2.72 - 3.27: 11964 3.27 - 3.81: 17870 3.81 - 4.36: 21662 4.36 - 4.90: 36919 Nonbonded interactions: 88896 Sorted by model distance: nonbonded pdb=" OD2 ASP B 471 " pdb="CA CA B 801 " model vdw 2.176 2.510 nonbonded pdb=" O ASN A 149 " pdb="CA CA A 801 " model vdw 2.202 2.510 nonbonded pdb=" O ASN C 149 " pdb="CA CA C 801 " model vdw 2.205 2.510 nonbonded pdb=" OD2 ASP C 471 " pdb="CA CA C 801 " model vdw 2.232 2.510 nonbonded pdb=" O THR B 61 " pdb=" OG SER B 62 " model vdw 2.247 3.040 ... (remaining 88891 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 50 through 801) selection = chain 'B' selection = chain 'C' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 0.213 10971 Z= 0.326 Angle : 0.769 15.991 14982 Z= 0.480 Chirality : 0.046 0.412 1824 Planarity : 0.010 0.206 1812 Dihedral : 11.500 87.839 3729 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.07 % Allowed : 6.48 % Favored : 91.45 % Cbeta Deviations : 0.23 % 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: 0.78 (0.23), residues: 1353 helix: 1.02 (0.16), residues: 981 sheet: None (None), residues: 0 loop : -0.68 (0.36), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 416 TYR 0.017 0.001 TYR C 557 PHE 0.020 0.002 PHE C 407 TRP 0.016 0.002 TRP C 317 HIS 0.032 0.006 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.32 (10962) covalent geometry : angle 0.76943 / 0.48 (14970) SS BOND : bond 0.00029 / 0.02 ( 6) SS BOND : angle 0.61784 / 0.32 ( 12) hydrogen bonds : bond 0.11932 / 7.68 ( 786) hydrogen bonds : angle 5.93344 / 4.35 ( 2286) metal coordination : bond 0.12416 / 6.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 121 PHE cc_start: 0.7327 (m-80) cc_final: 0.6921 (m-80) REVERT: A 149 ASN cc_start: 0.7974 (m-40) cc_final: 0.7633 (m-40) REVERT: A 221 TYR cc_start: 0.7599 (t80) cc_final: 0.7300 (t80) REVERT: A 518 GLU cc_start: 0.7093 (pt0) cc_final: 0.6774 (pt0) REVERT: B 445 ARG cc_start: 0.7255 (ttp80) cc_final: 0.7002 (ttp-110) REVERT: B 467 ASN cc_start: 0.7806 (m110) cc_final: 0.7520 (m110) REVERT: B 573 LEU cc_start: 0.7447 (mt) cc_final: 0.7208 (mt) REVERT: C 70 ARG cc_start: 0.6407 (ttp80) cc_final: 0.6124 (ttp80) REVERT: C 83 TYR cc_start: 0.7640 (m-80) cc_final: 0.7140 (m-80) REVERT: C 208 PHE cc_start: 0.8124 (m-80) cc_final: 0.7816 (m-80) REVERT: C 224 ARG cc_start: 0.6953 (ptm160) cc_final: 0.6688 (ptm160) REVERT: C 445 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6799 (ttt-90) REVERT: C 469 ILE cc_start: 0.8531 (tp) cc_final: 0.8215 (mt) outliers start: 24 outliers final: 17 residues processed: 217 average time/residue: 0.1025 time to fit residues: 30.4382 Evaluate side-chains 187 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 359 ASN A 498 ASN B 125 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 498 ASN ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.176993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131807 restraints weight = 13433.673| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.59 r_work: 0.3362 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 10971 Z= 0.241 Angle : 0.725 12.540 14982 Z= 0.366 Chirality : 0.046 0.323 1824 Planarity : 0.005 0.041 1812 Dihedral : 7.367 53.960 1503 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.23 % Allowed : 9.33 % Favored : 86.44 % 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 are not related in a simple way. whole: 1.02 (0.23), residues: 1353 helix: 1.09 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -0.29 (0.39), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 54 TYR 0.019 0.002 TYR A 557 PHE 0.025 0.002 PHE B 217 TRP 0.019 0.001 TRP A 106 HIS 0.007 0.002 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (10962) covalent geometry : angle 0.71413 / 0.36 (14970) SS BOND : bond 0.01063 / 0.50 ( 6) SS BOND : angle 4.51580 / 2.31 ( 12) hydrogen bonds : bond 0.05269 / 3.42 ( 786) hydrogen bonds : angle 5.08172 / 3.71 ( 2286) metal coordination : bond 0.06603 / 3.33 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7857 (m-80) cc_final: 0.7178 (m-80) REVERT: A 110 LEU cc_start: 0.7542 (mm) cc_final: 0.7305 (mt) REVERT: A 121 PHE cc_start: 0.7395 (m-80) cc_final: 0.6890 (m-80) REVERT: A 200 ARG cc_start: 0.7689 (mtm-85) cc_final: 0.7385 (mtm-85) REVERT: A 221 TYR cc_start: 0.8038 (t80) cc_final: 0.7743 (t80) REVERT: A 433 ILE cc_start: 0.7593 (mm) cc_final: 0.7363 (mt) REVERT: B 53 CYS cc_start: 0.6393 (t) cc_final: 0.6069 (t) REVERT: B 200 ARG cc_start: 0.7493 (mtm-85) cc_final: 0.6968 (mtm180) REVERT: B 227 LEU cc_start: 0.7745 (tp) cc_final: 0.7465 (tp) REVERT: B 445 ARG cc_start: 0.7608 (ttp80) cc_final: 0.7361 (ttp-110) REVERT: B 480 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7261 (mmm-85) REVERT: B 508 LEU cc_start: 0.7603 (tp) cc_final: 0.7313 (tt) REVERT: B 573 LEU cc_start: 0.7439 (mt) cc_final: 0.7187 (mt) REVERT: C 70 ARG cc_start: 0.7112 (ttp80) cc_final: 0.6692 (ttp80) REVERT: C 200 ARG cc_start: 0.7182 (mtm-85) cc_final: 0.6972 (mtm-85) REVERT: C 224 ARG cc_start: 0.7512 (ptm160) cc_final: 0.7219 (ptm160) REVERT: C 445 ARG cc_start: 0.7281 (ttp80) cc_final: 0.6976 (ttt-90) REVERT: C 469 ILE cc_start: 0.8406 (tp) cc_final: 0.8051 (mt) outliers start: 49 outliers final: 39 residues processed: 218 average time/residue: 0.1035 time to fit residues: 30.6874 Evaluate side-chains 211 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 498 ASN Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 498 ASN Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.0980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 ASN ** C 581 HIS ** 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 = 0.4138 r_free = 0.4138 target = 0.178899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.133477 restraints weight = 13453.825| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.56 r_work: 0.3388 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10971 Z= 0.162 Angle : 0.633 8.942 14982 Z= 0.323 Chirality : 0.043 0.313 1824 Planarity : 0.005 0.037 1812 Dihedral : 7.162 56.005 1500 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.97 % Allowed : 10.62 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.23 (0.23), residues: 1353 helix: 1.26 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -0.29 (0.38), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 64 TYR 0.015 0.002 TYR A 557 PHE 0.019 0.001 PHE B 217 TRP 0.017 0.001 TRP A 106 HIS 0.006 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (10962) covalent geometry : angle 0.62803 / 0.32 (14970) SS BOND : bond 0.00228 / 0.10 ( 6) SS BOND : angle 2.89756 / 1.71 ( 12) hydrogen bonds : bond 0.04603 / 2.97 ( 786) hydrogen bonds : angle 4.97841 / 3.65 ( 2286) metal coordination : bond 0.04220 / 2.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 83 TYR cc_start: 0.7828 (m-80) cc_final: 0.7158 (m-80) REVERT: A 121 PHE cc_start: 0.7426 (m-80) cc_final: 0.6867 (m-80) REVERT: A 200 ARG cc_start: 0.7636 (mtm-85) cc_final: 0.7320 (mtm-85) REVERT: A 221 TYR cc_start: 0.7937 (t80) cc_final: 0.7617 (t80) REVERT: A 433 ILE cc_start: 0.7590 (mm) cc_final: 0.7364 (mt) REVERT: A 480 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7332 (mtm-85) REVERT: B 200 ARG cc_start: 0.7471 (mtm-85) cc_final: 0.6957 (mtm180) REVERT: B 227 LEU cc_start: 0.7731 (tp) cc_final: 0.7459 (tp) REVERT: B 445 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7325 (ttp-110) REVERT: B 480 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7238 (mmm-85) REVERT: B 485 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7926 (mtm180) REVERT: B 508 LEU cc_start: 0.7571 (tp) cc_final: 0.7270 (tt) REVERT: B 573 LEU cc_start: 0.7424 (mt) cc_final: 0.7194 (mt) REVERT: C 70 ARG cc_start: 0.7062 (ttp80) cc_final: 0.6612 (ttp80) REVERT: C 200 ARG cc_start: 0.7158 (mtm-85) cc_final: 0.6951 (mtm-85) REVERT: C 224 ARG cc_start: 0.7471 (ptm160) cc_final: 0.7176 (ptm160) REVERT: C 445 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6925 (ttt-90) REVERT: C 469 ILE cc_start: 0.8337 (tp) cc_final: 0.7976 (mt) outliers start: 46 outliers final: 35 residues processed: 211 average time/residue: 0.0940 time to fit residues: 27.0508 Evaluate side-chains 211 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 8 optimal weight: 0.0770 chunk 4 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** 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 = 0.4131 r_free = 0.4131 target = 0.179275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132814 restraints weight = 13428.162| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.58 r_work: 0.3399 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10971 Z= 0.158 Angle : 0.613 8.967 14982 Z= 0.308 Chirality : 0.042 0.287 1824 Planarity : 0.004 0.037 1812 Dihedral : 6.928 59.522 1500 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.06 % Allowed : 11.74 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.11 (0.23), residues: 1353 helix: 1.23 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.60 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.020 0.002 TYR C 233 PHE 0.019 0.001 PHE A 217 TRP 0.012 0.001 TRP B 106 HIS 0.006 0.001 HIS A 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10962) covalent geometry : angle 0.60886 / 0.31 (14970) SS BOND : bond 0.00192 / 0.07 ( 6) SS BOND : angle 2.62552 / 1.46 ( 12) hydrogen bonds : bond 0.04353 / 2.81 ( 786) hydrogen bonds : angle 4.85997 / 3.56 ( 2286) metal coordination : bond 0.04427 / 2.22 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.247 Fit side-chains REVERT: A 50 MET cc_start: 0.4845 (tmm) cc_final: 0.4633 (tmm) REVERT: A 83 TYR cc_start: 0.7719 (m-80) cc_final: 0.7051 (m-80) REVERT: A 121 PHE cc_start: 0.7619 (m-80) cc_final: 0.7249 (m-80) REVERT: A 200 ARG cc_start: 0.7682 (mtm-85) cc_final: 0.7393 (mtm-85) REVERT: A 221 TYR cc_start: 0.7889 (t80) cc_final: 0.7598 (t80) REVERT: A 433 ILE cc_start: 0.7565 (mm) cc_final: 0.7362 (mt) REVERT: A 480 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7394 (mtm-85) REVERT: B 200 ARG cc_start: 0.7512 (mtm-85) cc_final: 0.7019 (mtm180) REVERT: B 227 LEU cc_start: 0.7698 (tp) cc_final: 0.7430 (tp) REVERT: B 445 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7322 (ttp-110) REVERT: B 480 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7326 (mtm-85) REVERT: B 485 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7930 (mtm180) REVERT: B 508 LEU cc_start: 0.7646 (tp) cc_final: 0.7360 (tt) REVERT: B 573 LEU cc_start: 0.7431 (mt) cc_final: 0.7221 (mt) REVERT: C 70 ARG cc_start: 0.7004 (ttp80) cc_final: 0.6685 (ttp80) REVERT: C 224 ARG cc_start: 0.7365 (ptm160) cc_final: 0.7133 (ptm160) REVERT: C 445 ARG cc_start: 0.7251 (ttp80) cc_final: 0.7003 (ttt-90) outliers start: 47 outliers final: 35 residues processed: 209 average time/residue: 0.1017 time to fit residues: 28.9673 Evaluate side-chains 208 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 0.0980 chunk 28 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 467 ASN ** C 581 HIS ** 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 = 0.4145 r_free = 0.4145 target = 0.179278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.133936 restraints weight = 13375.791| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.58 r_work: 0.3391 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10971 Z= 0.151 Angle : 0.606 8.314 14982 Z= 0.303 Chirality : 0.042 0.244 1824 Planarity : 0.004 0.038 1812 Dihedral : 6.377 57.705 1493 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.23 % Allowed : 13.30 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.12 (0.23), residues: 1353 helix: 1.26 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.71 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 200 TYR 0.018 0.001 TYR C 233 PHE 0.018 0.001 PHE A 217 TRP 0.013 0.001 TRP B 106 HIS 0.006 0.001 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (10962) covalent geometry : angle 0.60320 / 0.30 (14970) SS BOND : bond 0.00083 / 0.04 ( 6) SS BOND : angle 2.29915 / 1.31 ( 12) hydrogen bonds : bond 0.04215 / 2.74 ( 786) hydrogen bonds : angle 4.81352 / 3.52 ( 2286) metal coordination : bond 0.04547 / 2.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.240 Fit side-chains REVERT: A 50 MET cc_start: 0.4866 (tmm) cc_final: 0.4653 (tmm) REVERT: A 83 TYR cc_start: 0.7726 (m-80) cc_final: 0.7077 (m-80) REVERT: A 121 PHE cc_start: 0.7616 (m-80) cc_final: 0.7327 (m-80) REVERT: A 149 ASN cc_start: 0.7730 (m-40) cc_final: 0.7376 (m-40) REVERT: A 200 ARG cc_start: 0.7638 (mtm-85) cc_final: 0.7272 (mtm-85) REVERT: A 221 TYR cc_start: 0.7922 (t80) cc_final: 0.7606 (t80) REVERT: A 480 ARG cc_start: 0.7645 (mmm-85) cc_final: 0.7417 (mtm-85) REVERT: B 83 TYR cc_start: 0.7906 (m-80) cc_final: 0.7514 (m-80) REVERT: B 200 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.6957 (mtm180) REVERT: B 227 LEU cc_start: 0.7695 (tp) cc_final: 0.7463 (tp) REVERT: B 445 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7321 (ttp-110) REVERT: B 480 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7261 (mtm-85) REVERT: B 485 ARG cc_start: 0.8174 (mtp85) cc_final: 0.7922 (mtm180) REVERT: B 508 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7343 (tt) REVERT: B 573 LEU cc_start: 0.7440 (mt) cc_final: 0.7216 (mt) REVERT: C 70 ARG cc_start: 0.6926 (ttp80) cc_final: 0.6564 (ttp80) REVERT: C 224 ARG cc_start: 0.7436 (ptm160) cc_final: 0.7164 (ptm160) REVERT: C 445 ARG cc_start: 0.7246 (ttp80) cc_final: 0.6966 (ttt-90) REVERT: C 485 ARG cc_start: 0.7909 (mtp85) cc_final: 0.7588 (mtm180) REVERT: C 495 ILE cc_start: 0.7712 (pt) cc_final: 0.7309 (pt) outliers start: 49 outliers final: 35 residues processed: 214 average time/residue: 0.0979 time to fit residues: 28.6272 Evaluate side-chains 215 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain B residue 583 LYS Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 467 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** 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 = 0.4129 r_free = 0.4129 target = 0.177898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.132277 restraints weight = 13475.315| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.57 r_work: 0.3373 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10971 Z= 0.218 Angle : 0.645 9.134 14982 Z= 0.323 Chirality : 0.044 0.259 1824 Planarity : 0.005 0.040 1812 Dihedral : 6.406 55.410 1493 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.09 % Allowed : 13.64 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.88 (0.22), residues: 1353 helix: 1.08 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.76 (0.36), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 200 TYR 0.019 0.002 TYR C 233 PHE 0.023 0.002 PHE A 217 TRP 0.015 0.001 TRP A 529 HIS 0.009 0.002 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (10962) covalent geometry : angle 0.63997 / 0.32 (14970) SS BOND : bond 0.00279 / 0.14 ( 6) SS BOND : angle 2.88866 / 1.61 ( 12) hydrogen bonds : bond 0.04674 / 3.04 ( 786) hydrogen bonds : angle 4.86479 / 3.56 ( 2286) metal coordination : bond 0.06804 / 3.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.235 Fit side-chains REVERT: A 50 MET cc_start: 0.4983 (tmm) cc_final: 0.4758 (tmm) REVERT: A 83 TYR cc_start: 0.7735 (m-80) cc_final: 0.7023 (m-80) REVERT: A 121 PHE cc_start: 0.7649 (m-80) cc_final: 0.7397 (m-80) REVERT: A 149 ASN cc_start: 0.7675 (m-40) cc_final: 0.7335 (m-40) REVERT: A 200 ARG cc_start: 0.7497 (mtm-85) cc_final: 0.7124 (mtm180) REVERT: A 221 TYR cc_start: 0.7966 (t80) cc_final: 0.7686 (t80) REVERT: A 315 ARG cc_start: 0.5742 (OUTLIER) cc_final: 0.5331 (tmm160) REVERT: A 480 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7459 (mtm-85) REVERT: B 200 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.6933 (mtm180) REVERT: B 227 LEU cc_start: 0.7741 (tp) cc_final: 0.7526 (tp) REVERT: B 239 PHE cc_start: 0.7214 (t80) cc_final: 0.6809 (t80) REVERT: B 315 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.5624 (tmm160) REVERT: B 445 ARG cc_start: 0.7530 (ttp80) cc_final: 0.7299 (ttp-110) REVERT: B 480 ARG cc_start: 0.7524 (mmm-85) cc_final: 0.7241 (mtm-85) REVERT: B 485 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7946 (mtm180) REVERT: B 508 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7355 (tt) REVERT: B 573 LEU cc_start: 0.7438 (mt) cc_final: 0.7207 (mt) REVERT: C 70 ARG cc_start: 0.7055 (ttp80) cc_final: 0.6679 (ttp80) REVERT: C 224 ARG cc_start: 0.7420 (ptm160) cc_final: 0.7122 (ptm160) REVERT: C 445 ARG cc_start: 0.7242 (ttp80) cc_final: 0.6970 (ttt-90) outliers start: 59 outliers final: 43 residues processed: 210 average time/residue: 0.0986 time to fit residues: 27.9514 Evaluate side-chains 222 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 315 ARG Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 93 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 74 optimal weight: 30.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** 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 = 0.4139 r_free = 0.4139 target = 0.179747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.133370 restraints weight = 13337.111| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.59 r_work: 0.3405 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10971 Z= 0.154 Angle : 0.602 8.745 14982 Z= 0.300 Chirality : 0.042 0.236 1824 Planarity : 0.004 0.038 1812 Dihedral : 6.263 54.738 1493 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.32 % Allowed : 15.20 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.05 (0.22), residues: 1353 helix: 1.23 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 70 TYR 0.016 0.001 TYR C 233 PHE 0.018 0.001 PHE C 217 TRP 0.012 0.001 TRP A 106 HIS 0.006 0.001 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (10962) covalent geometry : angle 0.59869 / 0.30 (14970) SS BOND : bond 0.00196 / 0.10 ( 6) SS BOND : angle 2.29322 / 1.28 ( 12) hydrogen bonds : bond 0.04182 / 2.71 ( 786) hydrogen bonds : angle 4.78829 / 3.50 ( 2286) metal coordination : bond 0.04479 / 2.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.278 Fit side-chains REVERT: A 50 MET cc_start: 0.4928 (tmm) cc_final: 0.4708 (tmm) REVERT: A 83 TYR cc_start: 0.7717 (m-80) cc_final: 0.7053 (m-80) REVERT: A 111 PHE cc_start: 0.7645 (m-10) cc_final: 0.7278 (m-10) REVERT: A 149 ASN cc_start: 0.7699 (m-40) cc_final: 0.7372 (m-40) REVERT: A 200 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.7186 (mtm180) REVERT: A 221 TYR cc_start: 0.7895 (t80) cc_final: 0.7616 (t80) REVERT: A 315 ARG cc_start: 0.5685 (OUTLIER) cc_final: 0.5302 (tmm160) REVERT: A 480 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7524 (mtm-85) REVERT: B 200 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.6998 (mtm180) REVERT: B 227 LEU cc_start: 0.7618 (tp) cc_final: 0.7404 (tp) REVERT: B 239 PHE cc_start: 0.7246 (t80) cc_final: 0.6938 (t80) REVERT: B 445 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7300 (ttp-110) REVERT: B 480 ARG cc_start: 0.7564 (mmm-85) cc_final: 0.7327 (mtm-85) REVERT: B 485 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7929 (mtm180) REVERT: B 508 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7359 (tt) REVERT: B 573 LEU cc_start: 0.7445 (mt) cc_final: 0.7243 (mt) REVERT: C 70 ARG cc_start: 0.6977 (ttp80) cc_final: 0.6608 (ttp80) REVERT: C 224 ARG cc_start: 0.7302 (ptm160) cc_final: 0.7094 (ptm160) outliers start: 50 outliers final: 36 residues processed: 206 average time/residue: 0.0922 time to fit residues: 25.7508 Evaluate side-chains 212 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 59 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 86 optimal weight: 0.0770 chunk 70 optimal weight: 8.9990 chunk 123 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** 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 = 0.4131 r_free = 0.4131 target = 0.179885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.133480 restraints weight = 13195.492| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.59 r_work: 0.3396 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10971 Z= 0.198 Angle : 0.632 8.810 14982 Z= 0.315 Chirality : 0.044 0.265 1824 Planarity : 0.005 0.040 1812 Dihedral : 6.274 55.039 1493 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.06 % Allowed : 15.46 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.91 (0.22), residues: 1353 helix: 1.13 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.83 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 200 TYR 0.018 0.001 TYR C 233 PHE 0.021 0.001 PHE A 217 TRP 0.026 0.001 TRP B 391 HIS 0.008 0.002 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (10962) covalent geometry : angle 0.62848 / 0.31 (14970) SS BOND : bond 0.00222 / 0.11 ( 6) SS BOND : angle 2.58712 / 1.46 ( 12) hydrogen bonds : bond 0.04477 / 2.90 ( 786) hydrogen bonds : angle 4.81507 / 3.52 ( 2286) metal coordination : bond 0.06157 / 3.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.234 Fit side-chains REVERT: A 83 TYR cc_start: 0.7720 (m-80) cc_final: 0.7034 (m-80) REVERT: A 149 ASN cc_start: 0.7708 (m-40) cc_final: 0.7372 (m-40) REVERT: A 221 TYR cc_start: 0.7857 (t80) cc_final: 0.7599 (t80) REVERT: A 480 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7529 (mtm-85) REVERT: B 200 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.6991 (mtm180) REVERT: B 227 LEU cc_start: 0.7631 (tp) cc_final: 0.7401 (tp) REVERT: B 239 PHE cc_start: 0.7254 (t80) cc_final: 0.6919 (t80) REVERT: B 445 ARG cc_start: 0.7521 (ttp80) cc_final: 0.7307 (ttp-110) REVERT: B 480 ARG cc_start: 0.7524 (mmm-85) cc_final: 0.7306 (mtm-85) REVERT: B 485 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7948 (mtm180) REVERT: B 508 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7386 (tt) REVERT: B 573 LEU cc_start: 0.7445 (mt) cc_final: 0.7244 (mt) REVERT: C 70 ARG cc_start: 0.6846 (ttp80) cc_final: 0.6497 (ttp80) REVERT: C 224 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7106 (ptm160) outliers start: 47 outliers final: 35 residues processed: 199 average time/residue: 0.0935 time to fit residues: 25.2648 Evaluate side-chains 210 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 77 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** 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 = 0.4133 r_free = 0.4133 target = 0.178787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132886 restraints weight = 13311.273| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.54 r_work: 0.3409 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10971 Z= 0.169 Angle : 0.610 8.744 14982 Z= 0.304 Chirality : 0.043 0.230 1824 Planarity : 0.004 0.039 1812 Dihedral : 6.186 55.211 1493 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.63 % Allowed : 16.41 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.03 (0.22), residues: 1353 helix: 1.23 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.84 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 200 TYR 0.016 0.001 TYR C 233 PHE 0.019 0.001 PHE A 217 TRP 0.021 0.001 TRP B 391 HIS 0.007 0.001 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (10962) covalent geometry : angle 0.60711 / 0.30 (14970) SS BOND : bond 0.00181 / 0.09 ( 6) SS BOND : angle 2.34297 / 1.31 ( 12) hydrogen bonds : bond 0.04235 / 2.75 ( 786) hydrogen bonds : angle 4.78372 / 3.50 ( 2286) metal coordination : bond 0.04963 / 2.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.223 Fit side-chains REVERT: A 83 TYR cc_start: 0.7717 (m-80) cc_final: 0.7051 (m-80) REVERT: A 149 ASN cc_start: 0.7707 (m-40) cc_final: 0.7357 (m-40) REVERT: A 200 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7193 (mtm180) REVERT: A 221 TYR cc_start: 0.7831 (t80) cc_final: 0.7561 (t80) REVERT: A 480 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7529 (mtm-85) REVERT: B 200 ARG cc_start: 0.7467 (mtm-85) cc_final: 0.6979 (mtm180) REVERT: B 227 LEU cc_start: 0.7606 (tp) cc_final: 0.7398 (tp) REVERT: B 239 PHE cc_start: 0.7256 (t80) cc_final: 0.6949 (t80) REVERT: B 445 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7305 (ttp-110) REVERT: B 480 ARG cc_start: 0.7552 (mmm-85) cc_final: 0.7324 (mtm-85) REVERT: B 485 ARG cc_start: 0.8197 (mtp85) cc_final: 0.7929 (mtm180) REVERT: B 508 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7368 (tt) REVERT: C 70 ARG cc_start: 0.6762 (ttp80) cc_final: 0.6415 (ttp80) REVERT: C 224 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7077 (ptm160) outliers start: 42 outliers final: 33 residues processed: 194 average time/residue: 0.0945 time to fit residues: 25.1144 Evaluate side-chains 205 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 100 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** 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 = 0.4131 r_free = 0.4131 target = 0.178875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132910 restraints weight = 13281.375| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.53 r_work: 0.3405 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10971 Z= 0.190 Angle : 0.629 8.951 14982 Z= 0.312 Chirality : 0.044 0.235 1824 Planarity : 0.005 0.039 1812 Dihedral : 6.016 51.031 1491 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.37 % Allowed : 16.84 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.96 (0.22), residues: 1353 helix: 1.17 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.85 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 200 TYR 0.017 0.001 TYR A 557 PHE 0.021 0.001 PHE A 217 TRP 0.022 0.001 TRP B 391 HIS 0.008 0.002 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.19 (10962) covalent geometry : angle 0.62549 / 0.31 (14970) SS BOND : bond 0.00210 / 0.11 ( 6) SS BOND : angle 2.50488 / 1.41 ( 12) hydrogen bonds : bond 0.04410 / 2.86 ( 786) hydrogen bonds : angle 4.80181 / 3.51 ( 2286) metal coordination : bond 0.05850 / 2.92 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.236 Fit side-chains REVERT: A 83 TYR cc_start: 0.7722 (m-80) cc_final: 0.7047 (m-80) REVERT: A 149 ASN cc_start: 0.7716 (m-40) cc_final: 0.7358 (m-40) REVERT: A 221 TYR cc_start: 0.7852 (t80) cc_final: 0.7574 (t80) REVERT: A 480 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7520 (mtm-85) REVERT: B 200 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.6974 (mtm180) REVERT: B 227 LEU cc_start: 0.7630 (tp) cc_final: 0.7417 (tp) REVERT: B 239 PHE cc_start: 0.7263 (t80) cc_final: 0.6943 (t80) REVERT: B 445 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7306 (ttp-110) REVERT: B 480 ARG cc_start: 0.7538 (mmm-85) cc_final: 0.7311 (mtm-85) REVERT: B 485 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7938 (mtm180) REVERT: B 508 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7393 (tt) REVERT: C 70 ARG cc_start: 0.6762 (ttp80) cc_final: 0.6412 (ttp80) REVERT: C 73 ASP cc_start: 0.7273 (t70) cc_final: 0.6630 (t0) REVERT: C 224 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7078 (ptm160) outliers start: 39 outliers final: 34 residues processed: 191 average time/residue: 0.1037 time to fit residues: 26.9720 Evaluate side-chains 205 residues out of total 1158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 426 PHE Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 498 ASN Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 581 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 224 ARG Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 426 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 581 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** 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 = 0.4132 r_free = 0.4132 target = 0.178520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132755 restraints weight = 13302.607| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.52 r_work: 0.3410 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10971 Z= 0.175 Angle : 0.615 9.046 14982 Z= 0.305 Chirality : 0.043 0.230 1824 Planarity : 0.004 0.039 1812 Dihedral : 5.938 49.494 1491 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.63 % Allowed : 16.67 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.18 (0.22), residues: 1353 helix: 1.29 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.68 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 200 TYR 0.016 0.001 TYR C 233 PHE 0.020 0.001 PHE A 217 TRP 0.021 0.001 TRP B 391 HIS 0.008 0.002 HIS C 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (10962) covalent geometry : angle 0.61142 / 0.30 (14970) SS BOND : bond 0.00201 / 0.10 ( 6) SS BOND : angle 2.36878 / 1.33 ( 12) hydrogen bonds : bond 0.04286 / 2.78 ( 786) hydrogen bonds : angle 4.79062 / 3.50 ( 2286) metal coordination : bond 0.05419 / 2.71 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.62 seconds wall clock time: 42 minutes 41.35 seconds (2561.35 seconds total)