Starting phenix.real_space_refine on Sun Jan 26 11:23:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz2_41731/01_2025/8tz2_41731_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz2_41731/01_2025/8tz2_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_41731/01_2025/8tz2_41731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz2_41731/01_2025/8tz2_41731.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz2_41731/01_2025/8tz2_41731_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz2_41731/01_2025/8tz2_41731_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 66 Unusual residues: {' NA': 2, 'LBN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 20.39, per 1000 atoms: 0.83 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: 6.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.82 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: 8.23 Time building geometry restraints manager: 7.66 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: 0.09 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.400 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 58.920 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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= 0.480 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP C 316 HIS 0.003 0.001 HIS A 367 PHE 0.015 0.001 PHE B 413 TYR 0.009 0.001 TYR B 231 ARG 0.002 0.000 ARG C 355 *********************** 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 : 1.711 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: 2.0866 time to fit residues: 563.5108 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 : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3636 r_free = 0.3636 target = 0.147381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104680 restraints weight = 35685.629| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.72 r_work: 0.2951 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2075 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= 0.160 Angle : 0.473 5.947 17313 Z= 0.252 Chirality : 0.036 0.118 1989 Planarity : 0.004 0.041 2097 Dihedral : 12.530 127.102 1830 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.87 % Allowed : 9.26 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : 0.25 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 316 HIS 0.003 0.001 HIS B 367 PHE 0.010 0.001 PHE C 279 TYR 0.009 0.001 TYR B 231 ARG 0.002 0.000 ARG C 589 *********************** 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 166 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7726 (mmt180) REVERT: C 201 LYS cc_start: 0.6753 (mptt) cc_final: 0.5928 (tttt) REVERT: C 222 LEU cc_start: 0.7979 (tp) cc_final: 0.7315 (mt) REVERT: C 305 MET cc_start: 0.8404 (mmm) cc_final: 0.8164 (mmp) REVERT: C 370 MET cc_start: 0.8576 (mtm) cc_final: 0.8272 (mtp) REVERT: C 430 MET cc_start: 0.8160 (mtt) cc_final: 0.7694 (mtt) REVERT: B 222 LEU cc_start: 0.7750 (tp) cc_final: 0.7410 (mt) REVERT: B 430 MET cc_start: 0.8335 (mtt) cc_final: 0.8134 (mtt) outliers start: 11 outliers final: 4 residues processed: 162 average time/residue: 1.8887 time to fit residues: 347.2569 Evaluate side-chains 151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 147 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099125 restraints weight = 36937.902| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.35 r_work: 0.2921 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2793 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= 0.195 Angle : 0.475 6.178 17313 Z= 0.252 Chirality : 0.036 0.122 1989 Planarity : 0.004 0.043 2097 Dihedral : 11.538 131.913 1830 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.35 % Allowed : 9.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.21), residues: 1593 helix: 2.90 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : 0.02 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 316 HIS 0.003 0.001 HIS B 367 PHE 0.013 0.001 PHE A 279 TYR 0.007 0.001 TYR B 231 ARG 0.002 0.000 ARG A 436 *********************** 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 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6732 (mptt) cc_final: 0.6110 (tttt) REVERT: C 201 LYS cc_start: 0.7011 (mptt) cc_final: 0.6268 (tttt) REVERT: C 204 GLN cc_start: 0.6884 (tt0) cc_final: 0.6676 (pt0) REVERT: C 222 LEU cc_start: 0.7960 (tp) cc_final: 0.7273 (mt) REVERT: C 305 MET cc_start: 0.8464 (mmm) cc_final: 0.8208 (mmp) REVERT: C 355 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7708 (ttt-90) REVERT: C 430 MET cc_start: 0.8263 (mtt) cc_final: 0.7719 (mtt) REVERT: B 222 LEU cc_start: 0.7870 (tp) cc_final: 0.7473 (mt) REVERT: B 305 MET cc_start: 0.8402 (mmp) cc_final: 0.8039 (mmt) REVERT: B 424 LEU cc_start: 0.8355 (tp) cc_final: 0.8079 (tm) outliers start: 17 outliers final: 10 residues processed: 169 average time/residue: 2.0447 time to fit residues: 389.9736 Evaluate side-chains 162 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 1.826 ------------------------------------------------------------------------------- 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 413 PHE 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 152 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.140864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.097242 restraints weight = 37510.738| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.37 r_work: 0.2902 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12744 Z= 0.220 Angle : 0.482 5.516 17313 Z= 0.254 Chirality : 0.037 0.141 1989 Planarity : 0.004 0.044 2097 Dihedral : 10.974 132.183 1830 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.50 % Allowed : 11.01 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.21), residues: 1593 helix: 2.84 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.18 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.003 0.001 HIS B 367 PHE 0.012 0.001 PHE A 279 TYR 0.006 0.001 TYR B 553 ARG 0.001 0.000 ARG C 436 *********************** 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 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6804 (mptt) cc_final: 0.6106 (tttt) REVERT: C 201 LYS cc_start: 0.7083 (mptt) cc_final: 0.6325 (tttt) REVERT: C 204 GLN cc_start: 0.6832 (tt0) cc_final: 0.6549 (pt0) REVERT: C 222 LEU cc_start: 0.8012 (tp) cc_final: 0.7337 (mt) REVERT: C 305 MET cc_start: 0.8430 (mmm) cc_final: 0.8205 (mmp) REVERT: C 355 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7734 (ttt-90) REVERT: C 430 MET cc_start: 0.8375 (mtt) cc_final: 0.7819 (mtt) REVERT: C 592 ASP cc_start: 0.7557 (m-30) cc_final: 0.7306 (m-30) REVERT: B 222 LEU cc_start: 0.7865 (tp) cc_final: 0.7412 (mt) REVERT: B 267 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: B 424 LEU cc_start: 0.8326 (tp) cc_final: 0.8090 (tm) outliers start: 19 outliers final: 12 residues processed: 171 average time/residue: 1.9691 time to fit residues: 379.6722 Evaluate side-chains 161 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 482 ASP Chi-restraints excluded: chain A residue 550 VAL 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 267 GLN Chi-restraints excluded: chain B residue 350 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3575 r_free = 0.3575 target = 0.141368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.098201 restraints weight = 37607.551| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.31 r_work: 0.2927 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3325 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= 0.220 Angle : 0.476 5.575 17313 Z= 0.252 Chirality : 0.037 0.121 1989 Planarity : 0.004 0.044 2097 Dihedral : 10.505 126.712 1830 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.74 % Allowed : 11.72 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.21), residues: 1593 helix: 2.82 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 316 HIS 0.003 0.001 HIS B 367 PHE 0.013 0.001 PHE A 279 TYR 0.006 0.001 TYR B 553 ARG 0.001 0.000 ARG B 133 *********************** 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 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7005 (mptt) cc_final: 0.6324 (tttt) REVERT: A 424 LEU cc_start: 0.8341 (tp) cc_final: 0.7998 (tm) REVERT: C 201 LYS cc_start: 0.7022 (mptt) cc_final: 0.6252 (tttt) REVERT: C 222 LEU cc_start: 0.8021 (tp) cc_final: 0.7351 (mt) REVERT: C 305 MET cc_start: 0.8453 (mmm) cc_final: 0.8235 (mmp) REVERT: C 355 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7795 (ttt-90) REVERT: C 430 MET cc_start: 0.8418 (mtt) cc_final: 0.7842 (mtt) REVERT: C 592 ASP cc_start: 0.7660 (m-30) cc_final: 0.7409 (m-30) REVERT: B 201 LYS cc_start: 0.6912 (mptt) cc_final: 0.6216 (tttt) REVERT: B 222 LEU cc_start: 0.7873 (tp) cc_final: 0.7397 (mt) outliers start: 22 outliers final: 15 residues processed: 170 average time/residue: 1.9682 time to fit residues: 375.3285 Evaluate side-chains 162 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 2.204 ------------------------------------------------------------------------------- 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 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 355 ARG 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 B residue 349 GLU Chi-restraints excluded: chain B residue 350 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 110 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 27 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3590 r_free = 0.3590 target = 0.142594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099119 restraints weight = 36159.697| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.28 r_work: 0.2930 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3449 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= 0.205 Angle : 0.466 5.439 17313 Z= 0.247 Chirality : 0.036 0.121 1989 Planarity : 0.003 0.043 2097 Dihedral : 10.433 124.752 1830 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.98 % Allowed : 11.64 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.21), residues: 1593 helix: 2.86 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 150 HIS 0.003 0.001 HIS C 288 PHE 0.012 0.001 PHE C 279 TYR 0.006 0.001 TYR B 553 ARG 0.001 0.000 ARG B 133 *********************** 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 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6939 (mptt) cc_final: 0.6250 (tttt) REVERT: A 424 LEU cc_start: 0.8266 (tp) cc_final: 0.7910 (tm) REVERT: C 201 LYS cc_start: 0.6933 (mptt) cc_final: 0.6203 (tmmt) REVERT: C 222 LEU cc_start: 0.7989 (tp) cc_final: 0.7289 (mt) REVERT: C 305 MET cc_start: 0.8444 (mmm) cc_final: 0.8231 (mmp) REVERT: C 355 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7785 (ttt-90) REVERT: C 430 MET cc_start: 0.8458 (mtt) cc_final: 0.7847 (mtt) REVERT: C 489 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: C 592 ASP cc_start: 0.7624 (m-30) cc_final: 0.7382 (m-30) REVERT: B 201 LYS cc_start: 0.6848 (mptt) cc_final: 0.6149 (tttt) REVERT: B 267 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7894 (tt0) outliers start: 25 outliers final: 16 residues processed: 171 average time/residue: 1.9555 time to fit residues: 377.2896 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 : 1.785 ------------------------------------------------------------------------------- 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 482 ASP Chi-restraints excluded: chain A residue 537 SER Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 413 PHE 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 585 MET Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 349 GLU Chi-restraints excluded: chain B residue 350 SER 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 56 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3552 r_free = 0.3552 target = 0.139492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.095945 restraints weight = 36448.190| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.28 r_work: 0.2892 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12744 Z= 0.329 Angle : 0.543 6.748 17313 Z= 0.289 Chirality : 0.039 0.128 1989 Planarity : 0.004 0.048 2097 Dihedral : 10.701 124.822 1830 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.61 % Allowed : 11.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.21), residues: 1593 helix: 2.56 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 150 HIS 0.004 0.001 HIS C 288 PHE 0.016 0.001 PHE C 279 TYR 0.009 0.002 TYR A 483 ARG 0.002 0.000 ARG B 133 *********************** 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 193 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7051 (mptt) cc_final: 0.6304 (tttt) REVERT: A 424 LEU cc_start: 0.8327 (tp) cc_final: 0.8065 (tm) REVERT: C 201 LYS cc_start: 0.6871 (mptt) cc_final: 0.6131 (tmmt) REVERT: C 222 LEU cc_start: 0.8037 (tp) cc_final: 0.7366 (mt) REVERT: C 355 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7888 (ttt-90) REVERT: C 430 MET cc_start: 0.8539 (mtt) cc_final: 0.7906 (mtt) REVERT: C 489 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: C 592 ASP cc_start: 0.7704 (m-30) cc_final: 0.7409 (m-30) REVERT: B 222 LEU cc_start: 0.8144 (tt) cc_final: 0.7711 (mt) REVERT: B 267 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: B 313 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8242 (mt) outliers start: 33 outliers final: 17 residues processed: 185 average time/residue: 1.9462 time to fit residues: 405.1097 Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.962 ------------------------------------------------------------------------------- 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 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 355 ARG Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 413 PHE 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 B residue 149 VAL Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 350 SER 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 83 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 0.0000 chunk 87 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3595 r_free = 0.3595 target = 0.143025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.098778 restraints weight = 36292.749| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.35 r_work: 0.2924 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12744 Z= 0.175 Angle : 0.459 5.611 17313 Z= 0.242 Chirality : 0.036 0.119 1989 Planarity : 0.003 0.043 2097 Dihedral : 10.144 120.004 1830 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.58 % Allowed : 12.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.21), residues: 1593 helix: 2.86 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.34 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 150 HIS 0.002 0.001 HIS B 367 PHE 0.012 0.001 PHE C 279 TYR 0.008 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 *********************** 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 173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6976 (mptt) cc_final: 0.6245 (tttt) REVERT: A 424 LEU cc_start: 0.8215 (tp) cc_final: 0.7885 (tm) REVERT: C 201 LYS cc_start: 0.6788 (mptt) cc_final: 0.6068 (tmmt) REVERT: C 222 LEU cc_start: 0.7927 (tp) cc_final: 0.7227 (mt) REVERT: C 242 GLN cc_start: 0.8768 (mt0) cc_final: 0.8318 (mt0) REVERT: C 355 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7703 (ttt-90) REVERT: C 430 MET cc_start: 0.8479 (mtt) cc_final: 0.7885 (mtt) REVERT: C 489 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: C 592 ASP cc_start: 0.7622 (m-30) cc_final: 0.7371 (m-30) REVERT: B 201 LYS cc_start: 0.6865 (mptt) cc_final: 0.6092 (tttt) REVERT: B 222 LEU cc_start: 0.8060 (tt) cc_final: 0.7582 (mt) REVERT: B 267 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: B 482 ASP cc_start: 0.8094 (m-30) cc_final: 0.7864 (m-30) outliers start: 20 outliers final: 13 residues processed: 169 average time/residue: 1.8671 time to fit residues: 356.4127 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 : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 VAL 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 355 ARG 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 B residue 149 VAL Chi-restraints excluded: chain B residue 267 GLN 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 122 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: