Starting phenix.real_space_refine on Sun Jul 5 01:34:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz2_41731/07_2026/8tz2_41731_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz2_41731/07_2026/8tz2_41731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz2_41731/07_2026/8tz2_41731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz2_41731/07_2026/8tz2_41731.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz2_41731/07_2026/8tz2_41731_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz2_41731/07_2026/8tz2_41731_trim.cif" } resolution = 2.8 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= 0.002 sd= 0.089 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 S 87 5.16 5 Na 6 4.78 5 C 8256 2.51 5 N 1926 2.21 5 O 2145 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 24591 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'LBN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B Time building chain proxies: 9.66, per 1000 atoms: 0.39 Number of scatterers: 24591 At special positions: 0 Unit cell: (130.68, 127.44, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 6 15.00 Na 6 11.00 O 2145 8.00 N 1926 7.00 C 8256 6.00 H 12165 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 969.3 milliseconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 3 sheets defined 89.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 4.698A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.716A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.126A pdb=" N VAL A 230 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 4.392A pdb=" N GLY A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 294 through 312 Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.527A pdb=" N TRP A 316 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 349 through 361 Proline residue: A 356 - end of helix Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR A 385 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.258A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 479 removed outlier: 3.503A pdb=" N SER A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.607A pdb=" N TYR A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.116A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 3.709A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 574 through 586 Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.558A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 4.698A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.717A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 removed outlier: 4.126A pdb=" N VAL C 230 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 270 Processing helix chain 'C' and resid 272 through 282 removed outlier: 4.392A pdb=" N GLY C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.527A pdb=" N TRP C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 349 through 361 Proline residue: C 356 - end of helix Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR C 385 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.259A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 479 removed outlier: 3.504A pdb=" N SER C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.607A pdb=" N TYR C 494 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.116A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 3.708A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 574 through 586 Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.558A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 198 Proline residue: B 167 - end of helix removed outlier: 4.698A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.717A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.127A pdb=" N VAL B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.610A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 Processing helix chain 'B' and resid 272 through 282 removed outlier: 4.391A pdb=" N GLY B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 294 through 312 Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.526A pdb=" N TRP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 349 through 361 Proline residue: B 356 - end of helix Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.502A pdb=" N TYR B 385 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.258A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 479 removed outlier: 3.503A pdb=" N SER B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.607A pdb=" N TYR B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.116A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 3.709A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 574 through 586 Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.558A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 547 979 hydrogen bonds defined for protein. 2874 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: 5.86 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12147 1.03 - 1.22: 30 1.22 - 1.42: 5373 1.42 - 1.61: 7191 1.61 - 1.81: 168 Bond restraints: 24909 Sorted by residual: bond pdb=" O4 LBN A 804 " pdb=" P1 LBN A 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" O4 LBN B 804 " pdb=" P1 LBN B 804 " ideal model delta sigma weight residual 1.497 1.646 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" O4 LBN A 803 " pdb=" P1 LBN A 803 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O4 LBN B 803 " pdb=" P1 LBN B 803 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.47e+01 bond pdb=" O4 LBN C 804 " pdb=" P1 LBN C 804 " ideal model delta sigma weight residual 1.497 1.645 -0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 24904 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 44676 3.21 - 6.42: 132 6.42 - 9.64: 15 9.64 - 12.85: 6 12.85 - 16.06: 6 Bond angle restraints: 44835 Sorted by residual: angle pdb=" O1 LBN C 803 " pdb=" P1 LBN C 803 " pdb=" O2 LBN C 803 " ideal model delta sigma weight residual 93.45 109.51 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" O1 LBN A 803 " pdb=" P1 LBN A 803 " pdb=" O2 LBN A 803 " ideal model delta sigma weight residual 93.45 109.49 -16.04 3.00e+00 1.11e-01 2.86e+01 angle pdb=" O1 LBN A 804 " pdb=" P1 LBN A 804 " pdb=" O2 LBN A 804 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.85e+01 angle pdb=" O1 LBN B 803 " pdb=" P1 LBN B 803 " pdb=" O2 LBN B 803 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.84e+01 angle pdb=" O1 LBN B 804 " pdb=" P1 LBN B 804 " pdb=" O2 LBN B 804 " ideal model delta sigma weight residual 93.45 109.45 -16.00 3.00e+00 1.11e-01 2.84e+01 ... (remaining 44830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.57: 11442 32.57 - 65.14: 411 65.14 - 97.71: 9 97.71 - 130.28: 6 130.28 - 162.85: 6 Dihedral angle restraints: 11874 sinusoidal: 6144 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN C 804 " pdb=" C2 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.18 162.85 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O5 LBN A 804 " pdb=" C2 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.13 162.80 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O5 LBN B 804 " pdb=" C2 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " ideal model delta sinusoidal sigma weight residual 62.67 -100.10 162.77 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 11871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1390 0.038 - 0.075: 437 0.075 - 0.113: 153 0.113 - 0.150: 3 0.150 - 0.188: 6 Chirality restraints: 1989 Sorted by residual: chirality pdb=" C2 LBN C 804 " pdb=" C1 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" C2 LBN A 804 " pdb=" C1 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" C2 LBN B 804 " pdb=" C1 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.55 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1986 not shown) Planarity restraints: 3639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 195 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU B 195 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU B 195 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL B 196 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 195 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C LEU A 195 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU A 195 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 196 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 195 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C LEU C 195 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU C 195 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 196 " -0.014 2.00e-02 2.50e+03 ... (remaining 3636 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 956 2.18 - 2.79: 47350 2.79 - 3.39: 68133 3.39 - 4.00: 88119 4.00 - 4.60: 139696 Nonbonded interactions: 344254 Sorted by model distance: nonbonded pdb=" OE1 GLN C 206 " pdb=" H GLN C 206 " model vdw 1.581 2.450 nonbonded pdb=" OE1 GLN A 206 " pdb=" H GLN A 206 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLN B 206 " pdb=" H GLN B 206 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU B 525 " pdb=" H GLU B 525 " model vdw 1.642 2.450 nonbonded pdb=" OE1 GLU C 525 " pdb=" H GLU C 525 " model vdw 1.642 2.450 ... (remaining 344249 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.140 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 30.630 Find NCS groups from input model: 0.310 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: 0.010 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.007 0.149 12744 Z= 0.341 Angle : 0.753 16.062 17313 Z= 0.343 Chirality : 0.041 0.188 1989 Planarity : 0.004 0.036 2097 Dihedral : 15.024 162.847 4380 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: 3.08 (0.21), residues: 1593 helix: 2.46 (0.14), residues: 1326 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.009 0.001 TYR B 231 PHE 0.015 0.001 PHE B 413 TRP 0.015 0.001 TRP C 316 HIS 0.003 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00719 / 0.34 (12744) covalent geometry : angle 0.75274 / 0.34 (17313) hydrogen bonds : bond 0.13920 / 9.87 ( 979) hydrogen bonds : angle 5.35344 / 3.95 ( 2874) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 242 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7618 (mmt180) REVERT: C 222 LEU cc_start: 0.7957 (tp) cc_final: 0.7687 (mt) REVERT: B 222 LEU cc_start: 0.8096 (tp) cc_final: 0.7841 (mt) REVERT: B 430 MET cc_start: 0.7923 (mtt) cc_final: 0.7649 (mtt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.9144 time to fit residues: 247.9205 Evaluate side-chains 156 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.145175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099013 restraints weight = 36012.426| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.48 r_work: 0.2928 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12744 Z= 0.140 Angle : 0.491 5.662 17313 Z= 0.262 Chirality : 0.036 0.116 1989 Planarity : 0.004 0.044 2097 Dihedral : 12.717 128.545 1830 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.03 % Allowed : 9.34 % Favored : 89.63 % 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: 3.59 (0.21), residues: 1593 helix: 2.82 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : 0.20 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 589 TYR 0.008 0.001 TYR B 231 PHE 0.012 0.001 PHE C 279 TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (12744) covalent geometry : angle 0.49088 / 0.26 (17313) hydrogen bonds : bond 0.05416 / 3.72 ( 979) hydrogen bonds : angle 4.17342 / 3.09 ( 2874) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7747 (mmt180) REVERT: C 201 LYS cc_start: 0.6728 (mptt) cc_final: 0.5903 (tttt) REVERT: C 222 LEU cc_start: 0.7955 (tp) cc_final: 0.7298 (mt) REVERT: C 305 MET cc_start: 0.8428 (mmm) cc_final: 0.8192 (mmp) REVERT: C 370 MET cc_start: 0.8680 (mtm) cc_final: 0.8410 (mtp) REVERT: C 430 MET cc_start: 0.8188 (mtt) cc_final: 0.7679 (mtt) REVERT: B 222 LEU cc_start: 0.7728 (tp) cc_final: 0.7387 (mt) outliers start: 13 outliers final: 5 residues processed: 163 average time/residue: 0.8967 time to fit residues: 165.6734 Evaluate side-chains 151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 393 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 132 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.101005 restraints weight = 37028.995| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.38 r_work: 0.2963 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12744 Z= 0.115 Angle : 0.443 5.781 17313 Z= 0.234 Chirality : 0.035 0.121 1989 Planarity : 0.003 0.040 2097 Dihedral : 11.163 127.130 1830 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.50 % Allowed : 9.58 % Favored : 88.92 % 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: 3.87 (0.21), residues: 1593 helix: 3.04 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : 0.10 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 557 TYR 0.007 0.001 TYR B 231 PHE 0.010 0.001 PHE A 279 TRP 0.011 0.001 TRP B 316 HIS 0.002 0.001 HIS C 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12744) covalent geometry : angle 0.44320 / 0.23 (17313) hydrogen bonds : bond 0.04642 / 3.21 ( 979) hydrogen bonds : angle 3.85251 / 2.86 ( 2874) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6694 (mptt) cc_final: 0.6105 (tttt) REVERT: A 585 MET cc_start: 0.7450 (mtm) cc_final: 0.7235 (mtm) REVERT: C 201 LYS cc_start: 0.6934 (mptt) cc_final: 0.6189 (tttt) REVERT: C 222 LEU cc_start: 0.7934 (tp) cc_final: 0.7231 (mt) REVERT: C 305 MET cc_start: 0.8458 (mmm) cc_final: 0.8201 (mmp) REVERT: C 355 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7621 (ttt-90) REVERT: C 430 MET cc_start: 0.8251 (mtt) cc_final: 0.7743 (mtt) REVERT: B 222 LEU cc_start: 0.7820 (tp) cc_final: 0.7421 (mt) REVERT: B 305 MET cc_start: 0.8378 (mmp) cc_final: 0.7989 (mmt) outliers start: 19 outliers final: 9 residues processed: 171 average time/residue: 0.8879 time to fit residues: 171.6982 Evaluate side-chains 158 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 95 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 155 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.145351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102612 restraints weight = 36200.972| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.27 r_work: 0.2989 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12744 Z= 0.104 Angle : 0.431 5.175 17313 Z= 0.226 Chirality : 0.035 0.116 1989 Planarity : 0.003 0.037 2097 Dihedral : 10.371 129.282 1830 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.43 % Allowed : 10.77 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.01 (0.21), residues: 1593 helix: 3.17 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.01 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 557 TYR 0.006 0.001 TYR A 231 PHE 0.013 0.001 PHE A 146 TRP 0.009 0.001 TRP A 316 HIS 0.002 0.000 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (12744) covalent geometry : angle 0.43083 / 0.23 (17313) hydrogen bonds : bond 0.04205 / 2.89 ( 979) hydrogen bonds : angle 3.71729 / 2.76 ( 2874) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6740 (mptt) cc_final: 0.6081 (tttt) REVERT: A 242 GLN cc_start: 0.8531 (mt0) cc_final: 0.8314 (mt0) REVERT: A 585 MET cc_start: 0.7401 (mtm) cc_final: 0.7185 (mtt) REVERT: C 201 LYS cc_start: 0.6948 (mptt) cc_final: 0.6200 (tttt) REVERT: C 222 LEU cc_start: 0.7921 (tp) cc_final: 0.7216 (mt) REVERT: C 305 MET cc_start: 0.8413 (mmm) cc_final: 0.8168 (mmp) REVERT: C 430 MET cc_start: 0.8314 (mtt) cc_final: 0.7743 (mtt) REVERT: B 222 LEU cc_start: 0.7911 (tp) cc_final: 0.7465 (mt) REVERT: B 424 LEU cc_start: 0.8356 (tp) cc_final: 0.8136 (tm) outliers start: 18 outliers final: 12 residues processed: 164 average time/residue: 0.8788 time to fit residues: 164.0716 Evaluate side-chains 161 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 1 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 40.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.099342 restraints weight = 35948.323| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.29 r_work: 0.2936 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12744 Z= 0.147 Angle : 0.474 5.827 17313 Z= 0.251 Chirality : 0.036 0.121 1989 Planarity : 0.004 0.042 2097 Dihedral : 10.314 128.863 1830 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.90 % Allowed : 10.93 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.74 (0.21), residues: 1593 helix: 2.98 (0.14), residues: 1308 sheet: None (None), residues: 0 loop : -0.11 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 133 TYR 0.006 0.001 TYR C 285 PHE 0.013 0.001 PHE A 279 TRP 0.009 0.001 TRP A 316 HIS 0.003 0.001 HIS B 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (12744) covalent geometry : angle 0.47411 / 0.25 (17313) hydrogen bonds : bond 0.05218 / 3.59 ( 979) hydrogen bonds : angle 3.87551 / 2.87 ( 2874) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6939 (mptt) cc_final: 0.6262 (tttt) REVERT: A 424 LEU cc_start: 0.8233 (tp) cc_final: 0.7862 (tm) REVERT: A 585 MET cc_start: 0.7452 (mtm) cc_final: 0.7236 (mtt) REVERT: C 201 LYS cc_start: 0.6993 (mptt) cc_final: 0.6241 (tttt) REVERT: C 204 GLN cc_start: 0.6808 (tt0) cc_final: 0.6571 (pt0) REVERT: C 222 LEU cc_start: 0.7939 (tp) cc_final: 0.7244 (mt) REVERT: C 242 GLN cc_start: 0.8737 (mt0) cc_final: 0.8289 (mt0) REVERT: C 305 MET cc_start: 0.8397 (mmm) cc_final: 0.8173 (mmp) REVERT: C 430 MET cc_start: 0.8399 (mtt) cc_final: 0.7788 (mtt) REVERT: C 592 ASP cc_start: 0.7547 (m-30) cc_final: 0.7303 (m-30) REVERT: B 222 LEU cc_start: 0.7835 (tp) cc_final: 0.7357 (mt) REVERT: B 424 LEU cc_start: 0.8336 (tp) cc_final: 0.8112 (tm) outliers start: 24 outliers final: 20 residues processed: 177 average time/residue: 0.8848 time to fit residues: 177.9525 Evaluate side-chains 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 413 PHE Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 413 PHE Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 127 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.140337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.097028 restraints weight = 36443.510| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.27 r_work: 0.2908 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12744 Z= 0.185 Angle : 0.515 6.378 17313 Z= 0.274 Chirality : 0.038 0.125 1989 Planarity : 0.004 0.046 2097 Dihedral : 10.400 128.862 1830 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.14 % Allowed : 11.56 % Favored : 86.30 % 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: 3.36 (0.21), residues: 1593 helix: 2.73 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 436 TYR 0.009 0.002 TYR A 483 PHE 0.014 0.001 PHE A 279 TRP 0.007 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (12744) covalent geometry : angle 0.51521 / 0.27 (17313) hydrogen bonds : bond 0.05884 / 4.04 ( 979) hydrogen bonds : angle 4.02790 / 2.99 ( 2874) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6969 (mptt) cc_final: 0.6259 (tttt) REVERT: A 424 LEU cc_start: 0.8309 (tp) cc_final: 0.7947 (tm) REVERT: A 585 MET cc_start: 0.7481 (mtm) cc_final: 0.7253 (mtt) REVERT: C 201 LYS cc_start: 0.6943 (mptt) cc_final: 0.6214 (tmmt) REVERT: C 222 LEU cc_start: 0.8000 (tp) cc_final: 0.7322 (mt) REVERT: C 430 MET cc_start: 0.8490 (mtt) cc_final: 0.7881 (mtt) REVERT: C 489 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: C 592 ASP cc_start: 0.7627 (m-30) cc_final: 0.7347 (m-30) REVERT: B 222 LEU cc_start: 0.7881 (tp) cc_final: 0.7371 (mt) REVERT: B 305 MET cc_start: 0.8455 (mmp) cc_final: 0.8092 (mmt) REVERT: B 424 LEU cc_start: 0.8408 (tp) cc_final: 0.8168 (tm) outliers start: 27 outliers final: 19 residues processed: 179 average time/residue: 0.8888 time to fit residues: 180.6552 Evaluate side-chains 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 65 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.100101 restraints weight = 36235.637| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.29 r_work: 0.2944 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12744 Z= 0.121 Angle : 0.449 5.627 17313 Z= 0.238 Chirality : 0.036 0.121 1989 Planarity : 0.003 0.041 2097 Dihedral : 9.899 125.263 1830 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.74 % Allowed : 12.11 % Favored : 86.14 % 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: 3.68 (0.21), residues: 1593 helix: 2.96 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.23 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 251 TYR 0.006 0.001 TYR C 231 PHE 0.013 0.001 PHE C 146 TRP 0.008 0.001 TRP A 316 HIS 0.002 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (12744) covalent geometry : angle 0.44882 / 0.24 (17313) hydrogen bonds : bond 0.04698 / 3.23 ( 979) hydrogen bonds : angle 3.82850 / 2.84 ( 2874) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6947 (mptt) cc_final: 0.6247 (tttt) REVERT: A 424 LEU cc_start: 0.8270 (tp) cc_final: 0.7930 (tm) REVERT: A 585 MET cc_start: 0.7431 (mtm) cc_final: 0.7191 (mtt) REVERT: C 201 LYS cc_start: 0.6960 (mptt) cc_final: 0.6224 (tmmt) REVERT: C 222 LEU cc_start: 0.7961 (tp) cc_final: 0.7259 (mt) REVERT: C 242 GLN cc_start: 0.8714 (mt0) cc_final: 0.8279 (mt0) REVERT: C 430 MET cc_start: 0.8456 (mtt) cc_final: 0.7874 (mtt) REVERT: C 489 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: C 585 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6642 (mtt) REVERT: C 592 ASP cc_start: 0.7617 (m-30) cc_final: 0.7361 (m-30) REVERT: B 424 LEU cc_start: 0.8378 (tp) cc_final: 0.8148 (tm) outliers start: 22 outliers final: 17 residues processed: 173 average time/residue: 0.8867 time to fit residues: 173.3566 Evaluate side-chains 169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 100 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.097393 restraints weight = 36480.239| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.28 r_work: 0.2911 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12744 Z= 0.178 Angle : 0.503 6.041 17313 Z= 0.267 Chirality : 0.037 0.122 1989 Planarity : 0.004 0.045 2097 Dihedral : 10.086 125.082 1830 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.14 % Allowed : 11.80 % Favored : 86.06 % 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: 3.40 (0.21), residues: 1593 helix: 2.76 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.28 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 436 TYR 0.007 0.001 TYR A 483 PHE 0.014 0.001 PHE A 279 TRP 0.007 0.001 TRP A 316 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (12744) covalent geometry : angle 0.50263 / 0.27 (17313) hydrogen bonds : bond 0.05688 / 3.90 ( 979) hydrogen bonds : angle 3.98766 / 2.96 ( 2874) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7040 (mptt) cc_final: 0.6300 (tttt) REVERT: A 424 LEU cc_start: 0.8297 (tp) cc_final: 0.7938 (tm) REVERT: A 585 MET cc_start: 0.7456 (mtm) cc_final: 0.7221 (mtt) REVERT: C 201 LYS cc_start: 0.6998 (mptt) cc_final: 0.6260 (tmmt) REVERT: C 222 LEU cc_start: 0.8025 (tp) cc_final: 0.7341 (mt) REVERT: C 430 MET cc_start: 0.8499 (mtt) cc_final: 0.7866 (mtt) REVERT: C 489 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: C 592 ASP cc_start: 0.7683 (m-30) cc_final: 0.7421 (m-30) REVERT: B 222 LEU cc_start: 0.8079 (tt) cc_final: 0.7642 (mt) REVERT: B 305 MET cc_start: 0.8440 (mmp) cc_final: 0.8083 (mmt) REVERT: B 313 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 424 LEU cc_start: 0.8326 (tp) cc_final: 0.8074 (tm) outliers start: 27 outliers final: 18 residues processed: 179 average time/residue: 0.9199 time to fit residues: 185.7919 Evaluate side-chains 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.098601 restraints weight = 36599.523| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.36 r_work: 0.2921 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12744 Z= 0.137 Angle : 0.464 5.805 17313 Z= 0.245 Chirality : 0.036 0.120 1989 Planarity : 0.003 0.043 2097 Dihedral : 9.828 120.887 1830 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.90 % Allowed : 12.19 % Favored : 85.91 % 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: 3.58 (0.21), residues: 1593 helix: 2.90 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 355 TYR 0.007 0.001 TYR C 231 PHE 0.014 0.001 PHE C 146 TRP 0.008 0.001 TRP A 316 HIS 0.002 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12744) covalent geometry : angle 0.46395 / 0.25 (17313) hydrogen bonds : bond 0.04937 / 3.40 ( 979) hydrogen bonds : angle 3.87246 / 2.87 ( 2874) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6970 (mptt) cc_final: 0.6239 (tttt) REVERT: A 424 LEU cc_start: 0.8228 (tp) cc_final: 0.7867 (tm) REVERT: A 537 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7730 (m) REVERT: A 585 MET cc_start: 0.7394 (mtm) cc_final: 0.7157 (mtt) REVERT: C 201 LYS cc_start: 0.6834 (mptt) cc_final: 0.6109 (tttt) REVERT: C 222 LEU cc_start: 0.7938 (tp) cc_final: 0.7235 (mt) REVERT: C 342 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8801 (m-40) REVERT: C 430 MET cc_start: 0.8419 (mtt) cc_final: 0.7785 (mtt) REVERT: C 489 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: C 592 ASP cc_start: 0.7564 (m-30) cc_final: 0.7325 (m-30) REVERT: B 222 LEU cc_start: 0.8080 (tt) cc_final: 0.7587 (mt) REVERT: B 424 LEU cc_start: 0.8196 (tp) cc_final: 0.7926 (tm) outliers start: 24 outliers final: 16 residues processed: 175 average time/residue: 0.8957 time to fit residues: 176.8500 Evaluate side-chains 172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 46 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.143811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100421 restraints weight = 36233.270| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.28 r_work: 0.2950 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12744 Z= 0.119 Angle : 0.449 6.041 17313 Z= 0.237 Chirality : 0.035 0.118 1989 Planarity : 0.003 0.040 2097 Dihedral : 9.576 112.684 1830 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.50 % Allowed : 12.67 % Favored : 85.83 % 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: 3.77 (0.21), residues: 1593 helix: 3.03 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.22 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 251 TYR 0.007 0.001 TYR C 231 PHE 0.011 0.001 PHE C 279 TRP 0.009 0.001 TRP C 316 HIS 0.002 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (12744) covalent geometry : angle 0.44897 / 0.24 (17313) hydrogen bonds : bond 0.04577 / 3.15 ( 979) hydrogen bonds : angle 3.78734 / 2.81 ( 2874) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7022 (mptt) cc_final: 0.6310 (tttt) REVERT: A 424 LEU cc_start: 0.8273 (tp) cc_final: 0.7959 (tm) REVERT: A 537 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7755 (m) REVERT: C 201 LYS cc_start: 0.6987 (mptt) cc_final: 0.6272 (tttt) REVERT: C 222 LEU cc_start: 0.7966 (tp) cc_final: 0.7205 (mt) REVERT: C 430 MET cc_start: 0.8440 (mtt) cc_final: 0.7805 (mtt) REVERT: C 489 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: B 201 LYS cc_start: 0.6931 (mptt) cc_final: 0.6211 (tttt) REVERT: B 222 LEU cc_start: 0.8106 (tt) cc_final: 0.7615 (mt) REVERT: B 424 LEU cc_start: 0.8245 (tp) cc_final: 0.7994 (tm) outliers start: 19 outliers final: 14 residues processed: 167 average time/residue: 0.8827 time to fit residues: 166.1839 Evaluate side-chains 163 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 489 GLU Chi-restraints excluded: chain C residue 537 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 413 PHE Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 57 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.100091 restraints weight = 36377.214| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.29 r_work: 0.2946 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12744 Z= 0.123 Angle : 0.453 5.927 17313 Z= 0.239 Chirality : 0.036 0.118 1989 Planarity : 0.003 0.041 2097 Dihedral : 9.454 100.994 1830 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.43 % Allowed : 12.83 % Favored : 85.75 % 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: 3.79 (0.21), residues: 1593 helix: 3.04 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.20 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 251 TYR 0.006 0.001 TYR C 231 PHE 0.015 0.001 PHE A 146 TRP 0.008 0.001 TRP C 316 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12744) covalent geometry : angle 0.45294 / 0.24 (17313) hydrogen bonds : bond 0.04653 / 3.20 ( 979) hydrogen bonds : angle 3.79266 / 2.81 ( 2874) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7537.21 seconds wall clock time: 128 minutes 17.98 seconds (7697.98 seconds total)