Starting phenix.real_space_refine on Fri Jul 3 00:28:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vor_65225/07_2026/9vor_65225_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vor_65225/07_2026/9vor_65225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vor_65225/07_2026/9vor_65225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vor_65225/07_2026/9vor_65225.map" model { file = "/net/cci-nas-00/data/ceres_data/9vor_65225/07_2026/9vor_65225_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vor_65225/07_2026/9vor_65225_neut.cif" } resolution = 3.47 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 7143 2.51 5 N 1710 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10797 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4128 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 23, 'TRANS': 517} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 3, 'HIS:plan': 4, 'ASN:plan1': 4, 'GLU:plan': 5, 'PHE:plan': 2, 'TYR:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 123 Chain: "B" Number of atoms: 4127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4127 Classifications: {'peptide': 540} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 23, 'TRANS': 516} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 2, 'ASN:plan1': 3, 'GLU:plan': 5, 'PHE:plan': 2, 'TYR:plan': 3, 'ASP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 116 Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "E" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 355 Unusual residues: {'CLR': 11, 'PEE': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 306 Unusual residues: {'CLR': 9, 'PIE': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 2.83, per 1000 atoms: 0.26 Number of scatterers: 10797 At special positions: 0 Unit cell: (94.284, 96.903, 181.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 2 15.00 O 1876 8.00 N 1710 7.00 C 7143 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 272 " distance=2.04 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 354 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 352 " distance=2.04 Simple disulfide: pdb=" SG CYS A 337 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 395 " - pdb=" SG CYS A 402 " distance=2.02 Simple disulfide: pdb=" SG CYS A 399 " - pdb=" SG CYS A 408 " distance=2.03 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 354 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 337 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 395 " - pdb=" SG CYS B 402 " distance=2.03 Simple disulfide: pdb=" SG CYS B 399 " - pdb=" SG CYS B 408 " distance=2.03 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 99 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 99 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 383.3 milliseconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 39.3% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.664A pdb=" N LEU A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 80 through 87 removed outlier: 3.690A pdb=" N SER A 84 " --> pdb=" O MET A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 removed outlier: 3.970A pdb=" N SER A 91 " --> pdb=" O THR A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 137 removed outlier: 3.978A pdb=" N LEU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 removed outlier: 4.163A pdb=" N VAL A 161 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP A 162 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 441 Processing helix chain 'A' and resid 444 through 451 removed outlier: 4.021A pdb=" N SER A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 466 Processing helix chain 'A' and resid 470 through 474 removed outlier: 3.668A pdb=" N PHE A 474 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 495 removed outlier: 3.561A pdb=" N CYS A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 490 " --> pdb=" O TRP A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.745A pdb=" N THR A 514 " --> pdb=" O PHE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 549 removed outlier: 3.888A pdb=" N VAL A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 removed outlier: 3.610A pdb=" N GLU A 553 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 600 removed outlier: 3.661A pdb=" N TRP A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 593 " --> pdb=" O PHE A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 634 removed outlier: 3.865A pdb=" N VAL A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 620 " --> pdb=" O ALA A 616 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 664 removed outlier: 4.514A pdb=" N THR A 656 " --> pdb=" O HIS A 652 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VAL A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'B' and resid 67 through 76 removed outlier: 3.806A pdb=" N GLU B 76 " --> pdb=" O GLN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.779A pdb=" N TYR B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 139 removed outlier: 4.536A pdb=" N LEU B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N HIS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.725A pdb=" N TYR B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.533A pdb=" N SER B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 424 " --> pdb=" O ILE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 466 removed outlier: 4.078A pdb=" N LEU B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.589A pdb=" N PHE B 474 " --> pdb=" O ILE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 514 removed outlier: 3.548A pdb=" N CYS B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG B 485 " --> pdb=" O CYS B 481 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 490 " --> pdb=" O TRP B 486 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR B 500 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 501 " --> pdb=" O GLY B 497 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B 514 " --> pdb=" O PHE B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 549 removed outlier: 3.501A pdb=" N MET B 529 " --> pdb=" O ARG B 525 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 532 " --> pdb=" O ARG B 528 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 533 " --> pdb=" O MET B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 removed outlier: 4.010A pdb=" N GLU B 553 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 600 removed outlier: 3.557A pdb=" N GLU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 593 " --> pdb=" O PHE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 634 removed outlier: 3.954A pdb=" N VAL B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 662 removed outlier: 4.644A pdb=" N THR B 656 " --> pdb=" O HIS B 652 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL B 657 " --> pdb=" O LEU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.785A pdb=" N THR C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 203 removed outlier: 4.765A pdb=" N ASP A 307 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA A 174 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 305 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE A 176 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N VAL A 303 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET A 304 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 287 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 562 Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 203 removed outlier: 4.369A pdb=" N ASP B 307 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA B 174 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B 305 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE B 176 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 303 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLY B 302 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 287 " --> pdb=" O MET B 304 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 559 through 562 removed outlier: 3.569A pdb=" N PHE B 570 " --> pdb=" O GLY B 562 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.735A pdb=" N VAL C 13 " --> pdb=" O THR C 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 72 through 74 removed outlier: 3.895A pdb=" N SER C 74 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR C 83 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.572A pdb=" N TYR C 97 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C 116 " --> pdb=" O TYR C 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 13 through 14 removed outlier: 6.867A pdb=" N VAL E 13 " --> pdb=" O SER E 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 20 through 23 Processing sheet with id=AB2, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.513A pdb=" N TYR E 98 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR E 116 " --> pdb=" O TYR E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 51 through 52 removed outlier: 4.156A pdb=" N THR E 51 " --> pdb=" O ASP E 62 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1041 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: 1.50 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1616 1.32 - 1.44: 2990 1.44 - 1.57: 6398 1.57 - 1.70: 4 1.70 - 1.83: 94 Bond restraints: 11102 Sorted by residual: bond pdb=" C29 PIE B 810 " pdb=" C47 PIE B 810 " ideal model delta sigma weight residual 1.330 1.544 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C48 PIE B 810 " pdb=" C49 PIE B 810 " ideal model delta sigma weight residual 1.529 1.342 0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C39 PIE B 810 " pdb=" C40 PIE B 810 " ideal model delta sigma weight residual 1.524 1.340 0.184 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C51 PIE B 810 " pdb=" C52 PIE B 810 " ideal model delta sigma weight residual 1.523 1.341 0.182 2.00e-02 2.50e+03 8.29e+01 bond pdb=" C28 PIE B 810 " pdb=" C29 PIE B 810 " ideal model delta sigma weight residual 1.496 1.344 0.152 2.00e-02 2.50e+03 5.81e+01 ... (remaining 11097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 15065 3.25 - 6.50: 126 6.50 - 9.75: 11 9.75 - 13.00: 1 13.00 - 16.25: 2 Bond angle restraints: 15205 Sorted by residual: angle pdb=" C29 PIE B 810 " pdb=" C47 PIE B 810 " pdb=" C48 PIE B 810 " ideal model delta sigma weight residual 124.99 108.74 16.25 3.00e+00 1.11e-01 2.93e+01 angle pdb=" N ARG A 525 " pdb=" CA ARG A 525 " pdb=" C ARG A 525 " ideal model delta sigma weight residual 112.13 105.25 6.88 1.37e+00 5.33e-01 2.52e+01 angle pdb=" O11 PIE B 810 " pdb=" P PIE B 810 " pdb=" O14 PIE B 810 " ideal model delta sigma weight residual 94.58 108.24 -13.66 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C ALA A 356 " pdb=" CA ALA A 356 " pdb=" CB ALA A 356 " ideal model delta sigma weight residual 116.54 111.63 4.91 1.15e+00 7.56e-01 1.82e+01 angle pdb=" N GLY B 524 " pdb=" CA GLY B 524 " pdb=" C GLY B 524 " ideal model delta sigma weight residual 113.79 109.51 4.28 1.17e+00 7.31e-01 1.34e+01 ... (remaining 15200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.74: 7042 29.74 - 59.47: 441 59.47 - 89.21: 38 89.21 - 118.95: 7 118.95 - 148.68: 7 Dihedral angle restraints: 7535 sinusoidal: 3698 harmonic: 3837 Sorted by residual: dihedral pdb=" CB CYS A 481 " pdb=" SG CYS A 481 " pdb=" SG CYS A 573 " pdb=" CB CYS A 573 " ideal model delta sinusoidal sigma weight residual -86.00 -171.48 85.48 1 1.00e+01 1.00e-02 8.84e+01 dihedral pdb=" CB CYS B 481 " pdb=" SG CYS B 481 " pdb=" SG CYS B 573 " pdb=" CB CYS B 573 " ideal model delta sinusoidal sigma weight residual -86.00 -168.27 82.27 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 99 " pdb=" CB CYS C 99 " ideal model delta sinusoidal sigma weight residual 93.00 23.58 69.42 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 7532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.999: 1770 0.999 - 1.998: 0 1.998 - 2.997: 0 2.997 - 3.997: 0 3.997 - 4.996: 3 Chirality restraints: 1773 Sorted by residual: chirality pdb=" C2' PIE B 810 " pdb=" C1' PIE B 810 " pdb=" C3' PIE B 810 " pdb=" O2' PIE B 810 " both_signs ideal model delta sigma weight residual False -2.51 2.48 -5.00 2.00e-01 2.50e+01 6.24e+02 chirality pdb=" C1' PIE B 810 " pdb=" C2' PIE B 810 " pdb=" C6' PIE B 810 " pdb=" O1' PIE B 810 " both_signs ideal model delta sigma weight residual False -2.47 2.51 -4.99 2.00e-01 2.50e+01 6.22e+02 chirality pdb=" C2 PEE A 812 " pdb=" C1 PEE A 812 " pdb=" C3 PEE A 812 " pdb=" O2 PEE A 812 " both_signs ideal model delta sigma weight residual False -2.33 2.54 -4.87 2.00e-01 2.50e+01 5.93e+02 ... (remaining 1770 not shown) Planarity restraints: 1784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 PIE B 810 " 0.281 2.00e-02 2.50e+03 3.07e-01 9.43e+02 pdb=" C29 PIE B 810 " -0.502 2.00e-02 2.50e+03 pdb=" C47 PIE B 810 " 0.215 2.00e-02 2.50e+03 pdb=" C48 PIE B 810 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 467 " -0.036 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 468 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 468 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 468 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 467 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 468 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " 0.029 5.00e-02 4.00e+02 ... (remaining 1781 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2784 2.79 - 3.32: 11149 3.32 - 3.85: 16873 3.85 - 4.37: 19334 4.37 - 4.90: 31213 Nonbonded interactions: 81353 Sorted by model distance: nonbonded pdb=" OH TYR B 496 " pdb=" OE2 GLU B 620 " model vdw 2.265 3.040 nonbonded pdb=" O ASP A 81 " pdb=" OG SER A 84 " model vdw 2.324 3.040 nonbonded pdb=" O ALA A 616 " pdb=" OE1 GLU A 620 " model vdw 2.345 3.040 nonbonded pdb=" OH TYR A 496 " pdb=" OE2 GLU A 620 " model vdw 2.367 3.040 nonbonded pdb=" O ALA B 616 " pdb=" OE1 GLU B 620 " model vdw 2.369 3.040 ... (remaining 81348 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 66 through 205 or resid 261 through 352 or (resid 353 and \ (name N or name CA or name C or name O or name CB )) or resid 354 through 378 or \ (resid 379 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 0 through 524 or (resid 525 and (name N or name CA or name C or name O or name C \ B )) or resid 526 through 809)) selection = (chain 'B' and (resid 66 through 292 or resid 298 through 327 or (resid 328 and \ (name N or name CA or name C or name O or name CB )) or resid 329 through 331 or \ (resid 332 through 336 and (name N or name CA or name C or name O or name CB )) \ or resid 337 through 359 or (resid 360 and (name N or name CA or name C or name \ O or name CB )) or resid 361 through 362 or (resid 363 through 364 and (name N \ or name CA or name C or name O or name CB )) or resid 365 through 809)) } ncs_group { reference = (chain 'C' and ((resid 2 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or resid 3 through 122)) selection = chain 'E' } 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.010 0.782 11119 Z= 0.805 Angle : 0.836 16.251 15237 Z= 0.429 Chirality : 0.208 4.996 1773 Planarity : 0.009 0.307 1784 Dihedral : 17.811 148.683 5019 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.84 % Allowed : 16.96 % Favored : 82.19 % Rotamer: Outliers : 2.87 % Allowed : 27.44 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.11 (0.22), residues: 1303 helix: 0.11 (0.24), residues: 479 sheet: -2.28 (0.52), residues: 103 loop : -3.81 (0.20), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 196 TYR 0.022 0.002 TYR B 103 PHE 0.014 0.002 PHE B 467 TRP 0.012 0.002 TRP B 281 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.31 (11102) covalent geometry : angle 0.83460 / 0.43 (15205) SS BOND : bond 0.00408 / 0.28 ( 16) SS BOND : angle 1.30958 / 0.80 ( 32) hydrogen bonds : bond 0.14633 / 9.51 ( 371) hydrogen bonds : angle 6.84198 / 4.91 ( 1041) Misc. bond : bond 0.78154 / 41.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8373 (pmm) cc_final: 0.7633 (ppp) REVERT: A 149 ASN cc_start: 0.5550 (m110) cc_final: 0.4842 (t0) REVERT: A 156 TRP cc_start: 0.8284 (m100) cc_final: 0.7770 (m-10) REVERT: A 409 PHE cc_start: 0.7286 (t80) cc_final: 0.7015 (t80) REVERT: A 416 LEU cc_start: 0.8726 (mp) cc_final: 0.8101 (tt) REVERT: A 581 MET cc_start: 0.8656 (mmm) cc_final: 0.8243 (mmp) REVERT: B 178 PHE cc_start: 0.7138 (t80) cc_final: 0.6883 (t80) REVERT: B 520 TYR cc_start: 0.6236 (OUTLIER) cc_final: 0.5770 (m-80) REVERT: C 35 MET cc_start: 0.8097 (pmm) cc_final: 0.7734 (pmm) REVERT: C 101 TYR cc_start: 0.3675 (OUTLIER) cc_final: 0.1968 (m-80) REVERT: C 114 GLN cc_start: 0.6236 (tp40) cc_final: 0.5627 (tm-30) REVERT: E 56 ARG cc_start: 0.5846 (tpt170) cc_final: 0.5563 (tpt170) REVERT: E 79 LYS cc_start: 0.5569 (tttt) cc_final: 0.5252 (mttt) outliers start: 30 outliers final: 21 residues processed: 169 average time/residue: 0.0963 time to fit residues: 24.0923 Evaluate side-chains 156 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 447 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 118 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 628 HIS B 72 GLN B 143 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS E 6 GLN E 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.169995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116599 restraints weight = 23750.457| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.34 r_work: 0.3527 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11119 Z= 0.153 Angle : 0.724 8.064 15237 Z= 0.357 Chirality : 0.043 0.180 1773 Planarity : 0.005 0.051 1784 Dihedral : 11.539 134.145 2881 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.43 % Favored : 83.81 % Rotamer: Outliers : 4.49 % Allowed : 26.86 % Favored : 68.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.24), residues: 1303 helix: 0.98 (0.25), residues: 481 sheet: -2.42 (0.46), residues: 129 loop : -3.66 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.025 0.002 TYR E 104 PHE 0.015 0.002 PHE B 479 TRP 0.014 0.001 TRP E 57 HIS 0.006 0.001 HIS A 618 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11102) covalent geometry : angle 0.72231 / 0.36 (15205) SS BOND : bond 0.00324 / 0.22 ( 16) SS BOND : angle 1.19012 / 0.79 ( 32) hydrogen bonds : bond 0.05302 / 3.48 ( 371) hydrogen bonds : angle 4.93449 / 3.50 ( 1041) Misc. bond : bond 0.00018 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8385 (pmm) cc_final: 0.7802 (tmm) REVERT: A 149 ASN cc_start: 0.5617 (m110) cc_final: 0.4759 (t0) REVERT: A 156 TRP cc_start: 0.8221 (m100) cc_final: 0.7691 (m-10) REVERT: A 178 PHE cc_start: 0.7336 (t80) cc_final: 0.7071 (t80) REVERT: A 304 MET cc_start: 0.7733 (pmm) cc_final: 0.7441 (pmm) REVERT: A 409 PHE cc_start: 0.7569 (t80) cc_final: 0.7239 (t80) REVERT: A 416 LEU cc_start: 0.8777 (mp) cc_final: 0.8131 (tt) REVERT: A 492 PHE cc_start: 0.6127 (m-80) cc_final: 0.5337 (m-80) REVERT: A 528 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.5840 (tpt170) REVERT: A 581 MET cc_start: 0.8614 (mmm) cc_final: 0.8322 (mmp) REVERT: B 178 PHE cc_start: 0.7009 (t80) cc_final: 0.6709 (t80) REVERT: B 316 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6243 (t0) REVERT: B 466 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.6696 (t80) REVERT: B 520 TYR cc_start: 0.6110 (OUTLIER) cc_final: 0.5519 (m-80) REVERT: B 554 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7591 (mmtp) REVERT: B 644 LEU cc_start: 0.9200 (tp) cc_final: 0.8919 (tt) REVERT: C 35 MET cc_start: 0.8067 (pmm) cc_final: 0.7827 (pmm) REVERT: C 83 TYR cc_start: 0.5132 (p90) cc_final: 0.4908 (p90) REVERT: C 93 ASP cc_start: 0.6361 (t70) cc_final: 0.6039 (t0) REVERT: C 101 TYR cc_start: 0.3490 (OUTLIER) cc_final: 0.1568 (m-80) REVERT: C 104 TYR cc_start: 0.7655 (p90) cc_final: 0.7234 (p90) REVERT: C 114 GLN cc_start: 0.5678 (tp40) cc_final: 0.5230 (tm-30) REVERT: E 56 ARG cc_start: 0.6498 (tpt170) cc_final: 0.5835 (tpt170) REVERT: E 79 LYS cc_start: 0.5536 (tttt) cc_final: 0.5237 (mttt) REVERT: E 83 TYR cc_start: 0.5961 (p90) cc_final: 0.5549 (p90) outliers start: 47 outliers final: 26 residues processed: 185 average time/residue: 0.0920 time to fit residues: 25.4254 Evaluate side-chains 170 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 427 CYS Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 103 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 22 optimal weight: 0.8980 chunk 101 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.172089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.122363 restraints weight = 23741.486| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 4.07 r_work: 0.3541 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11119 Z= 0.126 Angle : 0.682 9.974 15237 Z= 0.338 Chirality : 0.043 0.263 1773 Planarity : 0.004 0.050 1784 Dihedral : 10.655 129.607 2868 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.04 % Favored : 84.27 % Rotamer: Outliers : 4.78 % Allowed : 27.53 % Favored : 67.69 % 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: -2.14 (0.24), residues: 1303 helix: 1.44 (0.26), residues: 480 sheet: -2.15 (0.49), residues: 119 loop : -3.61 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.021 0.001 TYR E 104 PHE 0.011 0.001 PHE A 178 TRP 0.012 0.001 TRP E 57 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (11102) covalent geometry : angle 0.68112 / 0.34 (15205) SS BOND : bond 0.00281 / 0.21 ( 16) SS BOND : angle 1.15145 / 0.77 ( 32) hydrogen bonds : bond 0.04299 / 2.85 ( 371) hydrogen bonds : angle 4.48000 / 3.19 ( 1041) Misc. bond : bond 0.00070 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 148 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8315 (pmm) cc_final: 0.7937 (tmm) REVERT: A 149 ASN cc_start: 0.5627 (m110) cc_final: 0.4981 (t0) REVERT: A 156 TRP cc_start: 0.8225 (m100) cc_final: 0.7668 (m-10) REVERT: A 178 PHE cc_start: 0.7457 (t80) cc_final: 0.7090 (t80) REVERT: A 304 MET cc_start: 0.7765 (pmm) cc_final: 0.7522 (pmm) REVERT: A 409 PHE cc_start: 0.7727 (t80) cc_final: 0.7453 (t80) REVERT: A 416 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 492 PHE cc_start: 0.6078 (m-80) cc_final: 0.5304 (m-80) REVERT: A 528 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.5744 (tpt170) REVERT: A 568 LEU cc_start: 0.8391 (mt) cc_final: 0.8172 (mm) REVERT: A 574 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7773 (mm) REVERT: B 178 PHE cc_start: 0.7045 (t80) cc_final: 0.6747 (t80) REVERT: B 316 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6268 (t0) REVERT: B 466 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.6752 (t80) REVERT: B 520 TYR cc_start: 0.6116 (OUTLIER) cc_final: 0.5605 (m-80) REVERT: B 554 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7584 (mmtp) REVERT: C 83 TYR cc_start: 0.5305 (p90) cc_final: 0.5100 (p90) REVERT: C 93 ASP cc_start: 0.6379 (t70) cc_final: 0.6104 (t0) REVERT: C 101 TYR cc_start: 0.3613 (OUTLIER) cc_final: 0.1647 (m-80) REVERT: C 104 TYR cc_start: 0.7679 (p90) cc_final: 0.7213 (p90) REVERT: C 114 GLN cc_start: 0.5449 (tp40) cc_final: 0.4885 (tm-30) REVERT: E 56 ARG cc_start: 0.6416 (tpt170) cc_final: 0.6057 (tpt170) REVERT: E 79 LYS cc_start: 0.5604 (tttt) cc_final: 0.5316 (tppt) REVERT: E 83 TYR cc_start: 0.6064 (p90) cc_final: 0.5740 (p90) REVERT: E 103 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7481 (p0) outliers start: 50 outliers final: 27 residues processed: 184 average time/residue: 0.0953 time to fit residues: 25.9723 Evaluate side-chains 172 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 124 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 143 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.171007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117697 restraints weight = 23657.997| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.34 r_work: 0.3544 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11119 Z= 0.141 Angle : 0.713 16.481 15237 Z= 0.346 Chirality : 0.043 0.185 1773 Planarity : 0.005 0.050 1784 Dihedral : 10.543 125.576 2863 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.89 % Favored : 83.35 % Rotamer: Outliers : 5.64 % Allowed : 28.11 % Favored : 66.25 % 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: -2.08 (0.24), residues: 1303 helix: 1.41 (0.25), residues: 483 sheet: -2.14 (0.48), residues: 129 loop : -3.54 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.022 0.002 TYR E 104 PHE 0.011 0.001 PHE A 538 TRP 0.011 0.001 TRP A 162 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (11102) covalent geometry : angle 0.71157 / 0.35 (15205) SS BOND : bond 0.00265 / 0.19 ( 16) SS BOND : angle 1.07113 / 0.71 ( 32) hydrogen bonds : bond 0.04539 / 3.01 ( 371) hydrogen bonds : angle 4.45830 / 3.17 ( 1041) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 MET cc_start: 0.8352 (pmm) cc_final: 0.7940 (tmm) REVERT: A 149 ASN cc_start: 0.5644 (m110) cc_final: 0.5007 (t0) REVERT: A 156 TRP cc_start: 0.8204 (m100) cc_final: 0.7676 (m-10) REVERT: A 178 PHE cc_start: 0.7685 (t80) cc_final: 0.7313 (t80) REVERT: A 409 PHE cc_start: 0.7795 (t80) cc_final: 0.7528 (t80) REVERT: A 416 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8047 (tt) REVERT: A 492 PHE cc_start: 0.6138 (m-80) cc_final: 0.5263 (m-80) REVERT: A 528 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.5852 (tpt170) REVERT: A 568 LEU cc_start: 0.8480 (mt) cc_final: 0.8264 (mm) REVERT: A 574 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7751 (mm) REVERT: B 178 PHE cc_start: 0.7224 (t80) cc_final: 0.6923 (t80) REVERT: B 316 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.6188 (t0) REVERT: B 466 TYR cc_start: 0.8108 (OUTLIER) cc_final: 0.6891 (t80) REVERT: B 520 TYR cc_start: 0.6064 (OUTLIER) cc_final: 0.5508 (m-80) REVERT: B 554 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7593 (mmtp) REVERT: C 4 GLN cc_start: 0.6673 (tp-100) cc_final: 0.6405 (tp-100) REVERT: C 35 MET cc_start: 0.7277 (pmm) cc_final: 0.6867 (pmm) REVERT: C 73 ILE cc_start: 0.5773 (OUTLIER) cc_final: 0.5514 (mt) REVERT: C 83 TYR cc_start: 0.5457 (p90) cc_final: 0.5227 (p90) REVERT: C 93 ASP cc_start: 0.6461 (t70) cc_final: 0.6144 (t0) REVERT: C 101 TYR cc_start: 0.3655 (OUTLIER) cc_final: 0.1639 (m-80) REVERT: C 104 TYR cc_start: 0.7531 (p90) cc_final: 0.7033 (p90) REVERT: C 114 GLN cc_start: 0.5431 (tp40) cc_final: 0.4844 (tm-30) REVERT: E 56 ARG cc_start: 0.6453 (tpt170) cc_final: 0.5802 (tpt170) REVERT: E 79 LYS cc_start: 0.5626 (tttt) cc_final: 0.5335 (mttt) REVERT: E 103 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7414 (p0) outliers start: 59 outliers final: 33 residues processed: 189 average time/residue: 0.0936 time to fit residues: 26.3201 Evaluate side-chains 181 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.0050 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.170968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117915 restraints weight = 23480.979| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.27 r_work: 0.3542 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11119 Z= 0.139 Angle : 0.703 14.151 15237 Z= 0.342 Chirality : 0.043 0.214 1773 Planarity : 0.005 0.049 1784 Dihedral : 10.505 125.865 2863 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.96 % Favored : 83.35 % Rotamer: Outliers : 6.41 % Allowed : 27.44 % Favored : 66.16 % 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: -2.06 (0.24), residues: 1303 helix: 1.45 (0.25), residues: 482 sheet: -2.19 (0.49), residues: 122 loop : -3.52 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 53 TYR 0.022 0.001 TYR E 104 PHE 0.010 0.001 PHE A 627 TRP 0.009 0.001 TRP A 162 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11102) covalent geometry : angle 0.70169 / 0.34 (15205) SS BOND : bond 0.00358 / 0.29 ( 16) SS BOND : angle 1.02140 / 0.70 ( 32) hydrogen bonds : bond 0.04434 / 2.93 ( 371) hydrogen bonds : angle 4.40454 / 3.14 ( 1041) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 144 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7403 (mp) REVERT: A 139 MET cc_start: 0.8331 (pmm) cc_final: 0.7977 (tmm) REVERT: A 156 TRP cc_start: 0.8205 (m100) cc_final: 0.7680 (m-10) REVERT: A 162 TRP cc_start: 0.7985 (t60) cc_final: 0.7731 (t60) REVERT: A 178 PHE cc_start: 0.7649 (t80) cc_final: 0.7330 (t80) REVERT: A 409 PHE cc_start: 0.7836 (t80) cc_final: 0.7502 (t80) REVERT: A 416 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.7964 (tt) REVERT: A 492 PHE cc_start: 0.6183 (m-80) cc_final: 0.5306 (m-80) REVERT: A 528 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.5792 (tpt170) REVERT: A 568 LEU cc_start: 0.8467 (mt) cc_final: 0.8252 (mm) REVERT: A 574 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7794 (mm) REVERT: B 178 PHE cc_start: 0.7245 (t80) cc_final: 0.6939 (t80) REVERT: B 316 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.6192 (t0) REVERT: B 401 PHE cc_start: 0.7968 (m-10) cc_final: 0.7656 (m-10) REVERT: B 416 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8241 (tt) REVERT: B 466 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.6851 (t80) REVERT: B 520 TYR cc_start: 0.6015 (OUTLIER) cc_final: 0.5456 (m-80) REVERT: B 554 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7603 (mmtp) REVERT: B 644 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8761 (tt) REVERT: C 4 GLN cc_start: 0.6819 (tp-100) cc_final: 0.6449 (tp-100) REVERT: C 35 MET cc_start: 0.7462 (pmm) cc_final: 0.6919 (pmm) REVERT: C 83 TYR cc_start: 0.5519 (p90) cc_final: 0.5221 (p90) REVERT: C 93 ASP cc_start: 0.6475 (t70) cc_final: 0.6168 (t0) REVERT: C 101 TYR cc_start: 0.3733 (OUTLIER) cc_final: 0.1595 (m-80) REVERT: C 104 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.6969 (p90) REVERT: C 114 GLN cc_start: 0.5747 (tp40) cc_final: 0.5158 (tm-30) REVERT: E 56 ARG cc_start: 0.6459 (tpt170) cc_final: 0.5871 (tpt170) REVERT: E 79 LYS cc_start: 0.5624 (tttt) cc_final: 0.5376 (mmtt) REVERT: E 83 TYR cc_start: 0.5845 (p90) cc_final: 0.5629 (p90) REVERT: E 103 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7377 (p0) outliers start: 67 outliers final: 35 residues processed: 197 average time/residue: 0.0877 time to fit residues: 25.4937 Evaluate side-chains 182 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 520 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS C 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.168278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.114481 restraints weight = 23620.031| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 3.32 r_work: 0.3499 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11119 Z= 0.198 Angle : 0.766 12.650 15237 Z= 0.375 Chirality : 0.045 0.245 1773 Planarity : 0.005 0.056 1784 Dihedral : 10.902 123.370 2863 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.69 % Allowed : 17.04 % Favored : 82.27 % Rotamer: Outliers : 6.12 % Allowed : 27.44 % Favored : 66.44 % 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: -2.26 (0.24), residues: 1303 helix: 1.20 (0.25), residues: 482 sheet: -2.12 (0.49), residues: 120 loop : -3.61 (0.21), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 53 TYR 0.022 0.002 TYR E 104 PHE 0.014 0.002 PHE B 467 TRP 0.012 0.001 TRP B 642 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (11102) covalent geometry : angle 0.76352 / 0.37 (15205) SS BOND : bond 0.00375 / 0.28 ( 16) SS BOND : angle 1.57058 / 1.01 ( 32) hydrogen bonds : bond 0.05235 / 3.46 ( 371) hydrogen bonds : angle 4.75433 / 3.39 ( 1041) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 137 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.6214 (mt) cc_final: 0.5799 (tt) REVERT: A 139 MET cc_start: 0.8363 (pmm) cc_final: 0.8031 (tmm) REVERT: A 156 TRP cc_start: 0.8307 (m100) cc_final: 0.7790 (m-10) REVERT: A 162 TRP cc_start: 0.8037 (t60) cc_final: 0.7793 (t60) REVERT: A 178 PHE cc_start: 0.7805 (t80) cc_final: 0.7484 (t80) REVERT: A 409 PHE cc_start: 0.8015 (t80) cc_final: 0.7668 (t80) REVERT: A 416 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8038 (tt) REVERT: A 528 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.5885 (tpt170) REVERT: A 568 LEU cc_start: 0.8478 (mt) cc_final: 0.8182 (mm) REVERT: A 574 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7820 (mm) REVERT: B 178 PHE cc_start: 0.7284 (t80) cc_final: 0.7000 (t80) REVERT: B 316 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.6359 (t0) REVERT: B 416 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8298 (tt) REVERT: B 554 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7706 (mmtp) REVERT: B 644 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8912 (tt) REVERT: C 4 GLN cc_start: 0.6924 (tp-100) cc_final: 0.6577 (tp-100) REVERT: C 35 MET cc_start: 0.7632 (pmm) cc_final: 0.6935 (pmm) REVERT: C 93 ASP cc_start: 0.6352 (t70) cc_final: 0.6043 (t0) REVERT: C 101 TYR cc_start: 0.3808 (OUTLIER) cc_final: 0.1662 (m-80) REVERT: C 104 TYR cc_start: 0.7493 (p90) cc_final: 0.6993 (p90) REVERT: C 114 GLN cc_start: 0.5968 (tp-100) cc_final: 0.5306 (tm-30) REVERT: E 56 ARG cc_start: 0.6558 (tpt170) cc_final: 0.5740 (tpt170) REVERT: E 79 LYS cc_start: 0.5457 (tttt) cc_final: 0.5205 (mttt) REVERT: E 83 TYR cc_start: 0.5816 (p90) cc_final: 0.5601 (p90) REVERT: E 103 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7500 (p0) outliers start: 64 outliers final: 41 residues processed: 192 average time/residue: 0.0889 time to fit residues: 25.2333 Evaluate side-chains 181 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 131 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 496 TYR Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 554 LYS Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 104 TYR Chi-restraints excluded: chain E residue 118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 50 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.171419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.118307 restraints weight = 23460.474| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.39 r_work: 0.3554 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11119 Z= 0.127 Angle : 0.707 12.157 15237 Z= 0.346 Chirality : 0.042 0.196 1773 Planarity : 0.005 0.053 1784 Dihedral : 10.354 125.211 2861 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.69 % Allowed : 16.12 % Favored : 83.19 % Rotamer: Outliers : 4.68 % Allowed : 29.25 % Favored : 66.06 % 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: -2.09 (0.24), residues: 1303 helix: 1.47 (0.26), residues: 482 sheet: -2.22 (0.49), residues: 122 loop : -3.57 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 53 TYR 0.021 0.001 TYR E 104 PHE 0.011 0.001 PHE A 627 TRP 0.010 0.001 TRP A 162 HIS 0.010 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11102) covalent geometry : angle 0.70506 / 0.35 (15205) SS BOND : bond 0.00272 / 0.20 ( 16) SS BOND : angle 1.31751 / 0.88 ( 32) hydrogen bonds : bond 0.04189 / 2.78 ( 371) hydrogen bonds : angle 4.38700 / 3.12 ( 1041) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 144 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.6146 (mt) cc_final: 0.5889 (tt) REVERT: A 156 TRP cc_start: 0.8273 (m100) cc_final: 0.7725 (m-10) REVERT: A 162 TRP cc_start: 0.8043 (t60) cc_final: 0.7770 (t60) REVERT: A 171 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6928 (pt) REVERT: A 178 PHE cc_start: 0.7761 (t80) cc_final: 0.7470 (t80) REVERT: A 409 PHE cc_start: 0.7978 (t80) cc_final: 0.7678 (t80) REVERT: A 416 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 492 PHE cc_start: 0.6141 (m-80) cc_final: 0.5214 (m-80) REVERT: A 528 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.5856 (tpt170) REVERT: A 574 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7823 (mm) REVERT: B 111 LYS cc_start: 0.3534 (tptp) cc_final: 0.3288 (tptt) REVERT: B 178 PHE cc_start: 0.7287 (t80) cc_final: 0.7015 (t80) REVERT: B 316 ASP cc_start: 0.6642 (OUTLIER) cc_final: 0.6222 (t0) REVERT: B 416 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8199 (tt) REVERT: B 466 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.6795 (t80) REVERT: C 4 GLN cc_start: 0.6961 (tp-100) cc_final: 0.6621 (tp-100) REVERT: C 35 MET cc_start: 0.7724 (pmm) cc_final: 0.7010 (pmm) REVERT: C 93 ASP cc_start: 0.6452 (t70) cc_final: 0.6142 (t0) REVERT: C 101 TYR cc_start: 0.3721 (OUTLIER) cc_final: 0.1630 (m-80) REVERT: C 104 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6909 (p90) REVERT: C 114 GLN cc_start: 0.5842 (tp-100) cc_final: 0.5407 (tm-30) REVERT: E 56 ARG cc_start: 0.6494 (tpt170) cc_final: 0.5985 (tpt170) REVERT: E 79 LYS cc_start: 0.5635 (tttt) cc_final: 0.5071 (tptt) REVERT: E 103 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7330 (p0) outliers start: 49 outliers final: 30 residues processed: 182 average time/residue: 0.0852 time to fit residues: 23.0151 Evaluate side-chains 174 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 627 PHE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 104 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 110 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 109 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS B 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.172067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.125545 restraints weight = 23753.631| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 4.22 r_work: 0.3586 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11119 Z= 0.124 Angle : 0.711 12.268 15237 Z= 0.346 Chirality : 0.042 0.180 1773 Planarity : 0.005 0.056 1784 Dihedral : 9.812 123.024 2855 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.77 % Allowed : 16.04 % Favored : 83.19 % Rotamer: Outliers : 4.21 % Allowed : 30.50 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.96 (0.25), residues: 1303 helix: 1.56 (0.26), residues: 486 sheet: -1.82 (0.51), residues: 117 loop : -3.58 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 53 TYR 0.020 0.001 TYR E 104 PHE 0.010 0.001 PHE A 627 TRP 0.010 0.001 TRP A 162 HIS 0.010 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (11102) covalent geometry : angle 0.70901 / 0.35 (15205) SS BOND : bond 0.00395 / 0.24 ( 16) SS BOND : angle 1.27287 / 0.87 ( 32) hydrogen bonds : bond 0.03836 / 2.54 ( 371) hydrogen bonds : angle 4.18944 / 2.98 ( 1041) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 144 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.6421 (mt) cc_final: 0.6150 (tt) REVERT: A 156 TRP cc_start: 0.8258 (m100) cc_final: 0.7693 (m-10) REVERT: A 162 TRP cc_start: 0.7992 (t60) cc_final: 0.7777 (t60) REVERT: A 409 PHE cc_start: 0.7986 (t80) cc_final: 0.7720 (t80) REVERT: A 416 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7903 (tt) REVERT: A 492 PHE cc_start: 0.6205 (m-80) cc_final: 0.5318 (m-80) REVERT: A 528 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.5890 (tpt170) REVERT: A 574 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7896 (mm) REVERT: B 121 SER cc_start: 0.8571 (p) cc_final: 0.8239 (t) REVERT: B 178 PHE cc_start: 0.7277 (t80) cc_final: 0.7023 (t80) REVERT: B 316 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6286 (t0) REVERT: B 466 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.6907 (t80) REVERT: C 4 GLN cc_start: 0.6998 (tp-100) cc_final: 0.6523 (tp-100) REVERT: C 35 MET cc_start: 0.7854 (pmm) cc_final: 0.7096 (pmm) REVERT: C 93 ASP cc_start: 0.6514 (t70) cc_final: 0.6204 (t0) REVERT: C 101 TYR cc_start: 0.3681 (OUTLIER) cc_final: 0.1512 (m-80) REVERT: C 104 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6868 (p90) REVERT: C 114 GLN cc_start: 0.5877 (tp-100) cc_final: 0.5410 (tm-30) REVERT: E 56 ARG cc_start: 0.6527 (tpt170) cc_final: 0.6078 (tpt170) REVERT: E 79 LYS cc_start: 0.5513 (tttt) cc_final: 0.5131 (tppt) REVERT: E 83 TYR cc_start: 0.5845 (p90) cc_final: 0.5433 (p90) REVERT: E 86 MET cc_start: 0.5624 (mmp) cc_final: 0.4319 (ttm) REVERT: E 103 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7498 (p0) outliers start: 44 outliers final: 29 residues processed: 178 average time/residue: 0.0871 time to fit residues: 22.9630 Evaluate side-chains 175 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 408 CYS Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 627 PHE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 104 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 130 optimal weight: 6.9990 chunk 118 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS B 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.172397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.124157 restraints weight = 23451.369| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 4.14 r_work: 0.3596 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11119 Z= 0.123 Angle : 0.712 11.214 15237 Z= 0.347 Chirality : 0.042 0.185 1773 Planarity : 0.005 0.056 1784 Dihedral : 9.650 120.578 2854 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.43 % Favored : 83.81 % Rotamer: Outliers : 3.63 % Allowed : 31.26 % Favored : 65.11 % 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: -1.88 (0.25), residues: 1303 helix: 1.63 (0.26), residues: 481 sheet: -1.87 (0.50), residues: 117 loop : -3.47 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 53 TYR 0.021 0.001 TYR E 104 PHE 0.010 0.001 PHE A 627 TRP 0.010 0.001 TRP A 162 HIS 0.010 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (11102) covalent geometry : angle 0.71076 / 0.35 (15205) SS BOND : bond 0.00251 / 0.19 ( 16) SS BOND : angle 1.20564 / 0.82 ( 32) hydrogen bonds : bond 0.03734 / 2.47 ( 371) hydrogen bonds : angle 4.14787 / 2.95 ( 1041) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.6476 (mt) cc_final: 0.6239 (tt) REVERT: A 168 GLU cc_start: 0.8165 (tp30) cc_final: 0.7848 (tp30) REVERT: A 409 PHE cc_start: 0.7977 (t80) cc_final: 0.7686 (t80) REVERT: A 416 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.7869 (tt) REVERT: A 492 PHE cc_start: 0.6192 (m-80) cc_final: 0.5309 (m-80) REVERT: A 528 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.5891 (tpt170) REVERT: A 574 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7844 (mm) REVERT: B 121 SER cc_start: 0.8433 (p) cc_final: 0.8120 (t) REVERT: B 178 PHE cc_start: 0.7320 (t80) cc_final: 0.7085 (t80) REVERT: B 316 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6188 (t0) REVERT: B 318 CYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5255 (m) REVERT: B 466 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.6873 (t80) REVERT: B 605 SER cc_start: 0.8512 (m) cc_final: 0.8179 (t) REVERT: C 4 GLN cc_start: 0.7122 (tp-100) cc_final: 0.6633 (tp-100) REVERT: C 35 MET cc_start: 0.7876 (pmm) cc_final: 0.7071 (pmm) REVERT: C 93 ASP cc_start: 0.6564 (t70) cc_final: 0.6228 (t0) REVERT: C 101 TYR cc_start: 0.3735 (OUTLIER) cc_final: 0.1570 (m-80) REVERT: C 104 TYR cc_start: 0.7392 (OUTLIER) cc_final: 0.6866 (p90) REVERT: C 114 GLN cc_start: 0.5939 (tp-100) cc_final: 0.5424 (tm-30) REVERT: E 56 ARG cc_start: 0.6543 (tpt170) cc_final: 0.6154 (tpt170) REVERT: E 79 LYS cc_start: 0.5549 (tttt) cc_final: 0.5159 (tppt) REVERT: E 86 MET cc_start: 0.5507 (mmp) cc_final: 0.4299 (ttm) REVERT: E 103 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7600 (p0) outliers start: 38 outliers final: 27 residues processed: 170 average time/residue: 0.0954 time to fit residues: 23.9386 Evaluate side-chains 175 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 627 PHE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 84 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 112 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS B 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.172643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.124866 restraints weight = 23501.340| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 3.81 r_work: 0.3618 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11119 Z= 0.123 Angle : 0.720 11.041 15237 Z= 0.349 Chirality : 0.042 0.190 1773 Planarity : 0.005 0.057 1784 Dihedral : 9.409 117.641 2854 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.73 % Favored : 83.50 % Rotamer: Outliers : 3.54 % Allowed : 31.36 % Favored : 65.11 % 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: -1.88 (0.25), residues: 1303 helix: 1.56 (0.26), residues: 490 sheet: -1.86 (0.51), residues: 116 loop : -3.48 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 53 TYR 0.021 0.001 TYR E 104 PHE 0.020 0.001 PHE A 178 TRP 0.010 0.001 TRP B 162 HIS 0.012 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11102) covalent geometry : angle 0.71879 / 0.35 (15205) SS BOND : bond 0.00270 / 0.20 ( 16) SS BOND : angle 1.14983 / 0.78 ( 32) hydrogen bonds : bond 0.03563 / 2.35 ( 371) hydrogen bonds : angle 4.05870 / 2.88 ( 1041) Misc. bond : bond 0.00013 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.6496 (mt) cc_final: 0.6273 (tt) REVERT: A 156 TRP cc_start: 0.8208 (m100) cc_final: 0.7642 (m-10) REVERT: A 168 GLU cc_start: 0.8172 (tp30) cc_final: 0.7887 (tp30) REVERT: A 409 PHE cc_start: 0.7831 (t80) cc_final: 0.7528 (t80) REVERT: A 416 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.7880 (tt) REVERT: A 492 PHE cc_start: 0.6085 (m-80) cc_final: 0.5181 (m-80) REVERT: A 528 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.5946 (tpt170) REVERT: A 574 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7845 (mm) REVERT: B 121 SER cc_start: 0.8392 (p) cc_final: 0.8052 (t) REVERT: B 178 PHE cc_start: 0.7348 (t80) cc_final: 0.7136 (t80) REVERT: B 316 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6169 (t0) REVERT: B 318 CYS cc_start: 0.5775 (OUTLIER) cc_final: 0.5220 (m) REVERT: B 466 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.6905 (t80) REVERT: B 605 SER cc_start: 0.8466 (m) cc_final: 0.8153 (t) REVERT: C 4 GLN cc_start: 0.7234 (tp-100) cc_final: 0.6768 (tp-100) REVERT: C 35 MET cc_start: 0.7811 (pmm) cc_final: 0.7072 (pmm) REVERT: C 93 ASP cc_start: 0.6572 (t70) cc_final: 0.6242 (t0) REVERT: C 101 TYR cc_start: 0.3740 (OUTLIER) cc_final: 0.1502 (m-80) REVERT: C 104 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6891 (p90) REVERT: C 114 GLN cc_start: 0.6017 (tp-100) cc_final: 0.5514 (tm-30) REVERT: E 56 ARG cc_start: 0.6526 (tpt170) cc_final: 0.6083 (tpt170) REVERT: E 79 LYS cc_start: 0.5563 (tttt) cc_final: 0.5155 (tppt) REVERT: E 86 MET cc_start: 0.5394 (mmp) cc_final: 0.4251 (ttm) REVERT: E 103 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7701 (p0) outliers start: 37 outliers final: 23 residues processed: 172 average time/residue: 0.0870 time to fit residues: 22.1855 Evaluate side-chains 173 residues out of total 1145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 528 ARG Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 620 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 466 TYR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 627 PHE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 101 TYR Chi-restraints excluded: chain C residue 104 TYR Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 104 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS B 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.172821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.121557 restraints weight = 23555.682| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 3.18 r_work: 0.3625 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11119 Z= 0.126 Angle : 0.728 10.925 15237 Z= 0.352 Chirality : 0.042 0.196 1773 Planarity : 0.005 0.053 1784 Dihedral : 9.344 115.002 2851 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.43 % Favored : 83.81 % Rotamer: Outliers : 3.73 % Allowed : 31.36 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.25), residues: 1303 helix: 1.56 (0.26), residues: 490 sheet: -1.73 (0.52), residues: 114 loop : -3.48 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 53 TYR 0.021 0.001 TYR E 104 PHE 0.010 0.001 PHE A 627 TRP 0.008 0.001 TRP B 162 HIS 0.012 0.001 HIS B 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (11102) covalent geometry : angle 0.72728 / 0.35 (15205) SS BOND : bond 0.00251 / 0.18 ( 16) SS BOND : angle 1.11333 / 0.76 ( 32) hydrogen bonds : bond 0.03716 / 2.40 ( 371) hydrogen bonds : angle 4.00258 / 2.85 ( 1041) Misc. bond : bond 0.00015 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.64 seconds wall clock time: 56 minutes 27.90 seconds (3387.90 seconds total)