Starting phenix.real_space_refine on Sat Jun 21 10:41:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz2_41731/06_2025/8tz2_41731_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz2_41731/06_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_41731/06_2025/8tz2_41731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz2_41731/06_2025/8tz2_41731.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz2_41731/06_2025/8tz2_41731_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz2_41731/06_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 21.94, per 1000 atoms: 0.89 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: 6.37 Conformation dependent library (CDL) restraints added in 2.1 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: 1.89 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: 9.59 Time building geometry restraints manager: 7.79 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: 1.030 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: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 63.390 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 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:13.370 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.840 ------------------------------------------------------------------------------- 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= 0.341 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13920 ( 979) hydrogen bonds : angle 5.35344 ( 2874) covalent geometry : bond 0.00719 (12744) covalent geometry : angle 0.75274 (17313) *********************** 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 : 1.671 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: 2.4749 time to fit residues: 677.2757 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 : 1.898 ------------------------------------------------------------------------------- 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 = 0.104679 restraints weight = 35685.580| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.72 r_work: 0.2951 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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= 0.123 Angle : 0.473 5.947 17313 Z= 0.252 Chirality : 0.036 0.118 1989 Planarity : 0.004 0.041 2097 Dihedral : 12.530 127.101 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 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 979) hydrogen bonds : angle 4.08503 ( 2874) covalent geometry : bond 0.00251 (12744) covalent geometry : angle 0.47341 (17313) *********************** 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 : 2.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7725 (mmt180) REVERT: C 201 LYS cc_start: 0.6738 (mptt) cc_final: 0.5914 (tttt) REVERT: C 222 LEU cc_start: 0.7976 (tp) cc_final: 0.7312 (mt) REVERT: C 305 MET cc_start: 0.8408 (mmm) cc_final: 0.8169 (mmp) REVERT: C 370 MET cc_start: 0.8573 (mtm) cc_final: 0.8267 (mtp) REVERT: C 430 MET cc_start: 0.8160 (mtt) cc_final: 0.7694 (mtt) REVERT: B 222 LEU cc_start: 0.7745 (tp) cc_final: 0.7406 (mt) REVERT: B 430 MET cc_start: 0.8334 (mtt) cc_final: 0.8132 (mtt) outliers start: 11 outliers final: 4 residues processed: 162 average time/residue: 1.8584 time to fit residues: 341.4944 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 : 1.825 ------------------------------------------------------------------------------- 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: 0.0000 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 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: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN 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 = 0.142862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099278 restraints weight = 36920.430| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.37 r_work: 0.2981 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12744 Z= 0.128 Angle : 0.458 5.539 17313 Z= 0.243 Chirality : 0.036 0.120 1989 Planarity : 0.003 0.041 2097 Dihedral : 11.387 130.303 1830 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.35 % Allowed : 9.82 % Favored : 88.84 % 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: 3.78 (0.21), residues: 1593 helix: 2.97 (0.14), residues: 1311 sheet: None (None), residues: 0 loop : 0.08 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.003 0.001 HIS C 367 PHE 0.012 0.001 PHE A 279 TYR 0.007 0.001 TYR B 231 ARG 0.002 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05012 ( 979) hydrogen bonds : angle 3.91095 ( 2874) covalent geometry : bond 0.00280 (12744) covalent geometry : angle 0.45820 (17313) *********************** 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 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6639 (mptt) cc_final: 0.6046 (tttt) REVERT: C 201 LYS cc_start: 0.6885 (mptt) cc_final: 0.6143 (tttt) REVERT: C 222 LEU cc_start: 0.7916 (tp) cc_final: 0.7211 (mt) REVERT: C 305 MET cc_start: 0.8411 (mmm) cc_final: 0.8146 (mmp) REVERT: C 355 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7274 (ttt-90) REVERT: C 430 MET cc_start: 0.8203 (mtt) cc_final: 0.7692 (mtt) REVERT: B 222 LEU cc_start: 0.7793 (tp) cc_final: 0.7394 (mt) outliers start: 17 outliers final: 10 residues processed: 168 average time/residue: 2.2289 time to fit residues: 422.6964 Evaluate side-chains 158 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 2.391 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 151 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.141649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.098428 restraints weight = 37470.119| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.32 r_work: 0.2942 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3131 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= 0.146 Angle : 0.484 5.601 17313 Z= 0.255 Chirality : 0.037 0.121 1989 Planarity : 0.004 0.044 2097 Dihedral : 10.943 132.653 1830 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.43 % Allowed : 11.16 % Favored : 87.41 % 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: 3.56 (0.21), residues: 1593 helix: 2.86 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.16 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 316 HIS 0.003 0.001 HIS B 367 PHE 0.014 0.001 PHE A 146 TYR 0.006 0.001 TYR C 285 ARG 0.001 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.05239 ( 979) hydrogen bonds : angle 3.94159 ( 2874) covalent geometry : bond 0.00332 (12744) covalent geometry : angle 0.48392 (17313) *********************** 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 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 3.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6908 (mptt) cc_final: 0.6238 (tttt) REVERT: A 585 MET cc_start: 0.7451 (mtm) cc_final: 0.7232 (mtt) REVERT: C 201 LYS cc_start: 0.7075 (mptt) cc_final: 0.6316 (tttt) REVERT: C 204 GLN cc_start: 0.6816 (tt0) cc_final: 0.6530 (pt0) REVERT: C 222 LEU cc_start: 0.7965 (tp) cc_final: 0.7277 (mt) REVERT: C 305 MET cc_start: 0.8444 (mmm) cc_final: 0.8211 (mmp) REVERT: C 355 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7700 (ttt-90) REVERT: C 430 MET cc_start: 0.8348 (mtt) cc_final: 0.7784 (mtt) REVERT: C 592 ASP cc_start: 0.7538 (m-30) cc_final: 0.7305 (m-30) REVERT: B 222 LEU cc_start: 0.7855 (tp) cc_final: 0.7393 (mt) REVERT: B 424 LEU cc_start: 0.8331 (tp) cc_final: 0.8114 (tm) outliers start: 18 outliers final: 12 residues processed: 172 average time/residue: 1.9527 time to fit residues: 379.7048 Evaluate side-chains 165 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.142651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.099846 restraints weight = 36407.933| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.26 r_work: 0.2946 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3305 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= 0.128 Angle : 0.454 5.331 17313 Z= 0.240 Chirality : 0.036 0.121 1989 Planarity : 0.003 0.041 2097 Dihedral : 10.415 126.539 1830 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.66 % Allowed : 11.72 % Favored : 86.62 % 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: 3.65 (0.21), residues: 1593 helix: 2.93 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.19 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.002 0.001 HIS B 367 PHE 0.011 0.001 PHE C 279 TYR 0.005 0.001 TYR A 216 ARG 0.001 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.04815 ( 979) hydrogen bonds : angle 3.83314 ( 2874) covalent geometry : bond 0.00286 (12744) covalent geometry : angle 0.45411 (17313) *********************** 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: 21 poor density : 154 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6936 (mptt) cc_final: 0.6272 (tttt) REVERT: A 242 GLN cc_start: 0.8637 (mt0) cc_final: 0.8381 (mt0) REVERT: A 424 LEU cc_start: 0.8249 (tp) cc_final: 0.7877 (tm) REVERT: C 201 LYS cc_start: 0.6860 (mptt) cc_final: 0.6098 (tttt) REVERT: C 204 GLN cc_start: 0.6815 (tt0) cc_final: 0.6514 (pt0) REVERT: C 222 LEU cc_start: 0.7917 (tp) cc_final: 0.7214 (mt) REVERT: C 305 MET cc_start: 0.8428 (mmm) cc_final: 0.8204 (mmp) REVERT: C 355 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7716 (ttt-90) REVERT: C 430 MET cc_start: 0.8402 (mtt) cc_final: 0.7799 (mtt) REVERT: C 585 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6501 (mtt) REVERT: B 222 LEU cc_start: 0.7792 (tp) cc_final: 0.7303 (mt) REVERT: B 424 LEU cc_start: 0.8324 (tp) cc_final: 0.8103 (tm) outliers start: 21 outliers final: 16 residues processed: 169 average time/residue: 1.9693 time to fit residues: 376.5509 Evaluate side-chains 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 3.097 ------------------------------------------------------------------------------- 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 C residue 585 MET Chi-restraints excluded: chain B residue 149 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 Chi-restraints excluded: chain B residue 439 LEU 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: 5.9990 chunk 5 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.141752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.097110 restraints weight = 36148.192| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.36 r_work: 0.2903 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12744 Z= 0.173 Angle : 0.497 5.962 17313 Z= 0.264 Chirality : 0.037 0.124 1989 Planarity : 0.004 0.045 2097 Dihedral : 10.613 126.696 1830 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.90 % Allowed : 11.72 % 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: 3.39 (0.21), residues: 1593 helix: 2.75 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.28 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 316 HIS 0.003 0.001 HIS C 288 PHE 0.014 0.001 PHE A 279 TYR 0.007 0.001 TYR A 483 ARG 0.001 0.000 ARG C 436 Details of bonding type rmsd hydrogen bonds : bond 0.05654 ( 979) hydrogen bonds : angle 3.97620 ( 2874) covalent geometry : bond 0.00406 (12744) covalent geometry : angle 0.49691 (17313) *********************** 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 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6912 (mptt) cc_final: 0.6213 (tttt) REVERT: A 424 LEU cc_start: 0.8272 (tp) cc_final: 0.7894 (tm) REVERT: C 201 LYS cc_start: 0.6884 (mptt) cc_final: 0.6161 (tmmt) REVERT: C 222 LEU cc_start: 0.7964 (tp) cc_final: 0.7283 (mt) REVERT: C 305 MET cc_start: 0.8445 (mmm) cc_final: 0.8218 (mmp) REVERT: C 355 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7778 (ttt-90) REVERT: C 430 MET cc_start: 0.8469 (mtt) cc_final: 0.7852 (mtt) REVERT: C 592 ASP cc_start: 0.7675 (m-30) cc_final: 0.7408 (m-30) REVERT: B 222 LEU cc_start: 0.7843 (tp) cc_final: 0.7320 (mt) REVERT: B 424 LEU cc_start: 0.8355 (tp) cc_final: 0.8109 (tm) outliers start: 24 outliers final: 15 residues processed: 177 average time/residue: 1.8699 time to fit residues: 372.2053 Evaluate side-chains 169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.816 ------------------------------------------------------------------------------- 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 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 C residue 620 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.138845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.095550 restraints weight = 36500.179| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.27 r_work: 0.2886 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 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 : 0.006 0.046 12744 Z= 0.234 Angle : 0.560 7.188 17313 Z= 0.299 Chirality : 0.040 0.170 1989 Planarity : 0.004 0.049 2097 Dihedral : 10.850 127.439 1830 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.38 % Allowed : 11.32 % 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 (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: 2.94 (0.21), residues: 1593 helix: 2.44 (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 0.005 0.001 TRP A 316 HIS 0.004 0.001 HIS C 288 PHE 0.016 0.002 PHE A 279 TYR 0.011 0.002 TYR A 483 ARG 0.002 0.000 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.06604 ( 979) hydrogen bonds : angle 4.19118 ( 2874) covalent geometry : bond 0.00562 (12744) covalent geometry : angle 0.55956 (17313) *********************** 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 191 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7061 (mptt) cc_final: 0.6295 (tttt) REVERT: A 424 LEU cc_start: 0.8372 (tp) cc_final: 0.8109 (tm) REVERT: C 201 LYS cc_start: 0.6903 (mptt) cc_final: 0.6169 (tttt) REVERT: C 222 LEU cc_start: 0.8040 (tp) cc_final: 0.7370 (mt) REVERT: C 355 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7916 (ttt-90) REVERT: C 430 MET cc_start: 0.8521 (mtt) cc_final: 0.7898 (mtt) REVERT: C 489 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: B 222 LEU cc_start: 0.7877 (tp) cc_final: 0.7342 (mt) REVERT: B 267 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: B 313 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8237 (mt) REVERT: B 424 LEU cc_start: 0.8393 (tp) cc_final: 0.8135 (tm) outliers start: 30 outliers final: 19 residues processed: 184 average time/residue: 1.8330 time to fit residues: 380.8924 Evaluate side-chains 181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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 C residue 620 ASN 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 342 ASN 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: 1.9990 chunk 18 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.143028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.099488 restraints weight = 36328.973| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.29 r_work: 0.2935 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12744 Z= 0.122 Angle : 0.456 5.451 17313 Z= 0.242 Chirality : 0.036 0.120 1989 Planarity : 0.003 0.043 2097 Dihedral : 10.272 123.593 1830 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.74 % Allowed : 12.59 % Favored : 85.67 % 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: 3.46 (0.21), residues: 1593 helix: 2.83 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.38 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.002 0.001 HIS B 367 PHE 0.013 0.001 PHE C 146 TYR 0.009 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 979) hydrogen bonds : angle 3.86733 ( 2874) covalent geometry : bond 0.00269 (12744) covalent geometry : angle 0.45638 (17313) *********************** 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 183 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7029 (mptt) cc_final: 0.6296 (tttt) REVERT: A 242 GLN cc_start: 0.8665 (mt0) cc_final: 0.8397 (mt0) REVERT: A 424 LEU cc_start: 0.8269 (tp) cc_final: 0.7944 (tm) REVERT: C 201 LYS cc_start: 0.6882 (mptt) cc_final: 0.6165 (tttt) REVERT: C 222 LEU cc_start: 0.7958 (tp) cc_final: 0.7262 (mt) REVERT: C 242 GLN cc_start: 0.8768 (mt0) cc_final: 0.8337 (mt0) REVERT: C 355 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7750 (ttt-90) REVERT: C 430 MET cc_start: 0.8478 (mtt) cc_final: 0.7863 (mtt) REVERT: C 489 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6534 (mp0) REVERT: C 592 ASP cc_start: 0.7659 (m-30) cc_final: 0.7386 (m-30) REVERT: B 267 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 424 LEU cc_start: 0.8212 (tp) cc_final: 0.7924 (tm) outliers start: 22 outliers final: 13 residues processed: 179 average time/residue: 1.8636 time to fit residues: 376.0731 Evaluate side-chains 169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 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=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: 8.9990 chunk 7 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 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: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.140043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096496 restraints weight = 36347.040| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.28 r_work: 0.2893 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12744 Z= 0.215 Angle : 0.540 6.584 17313 Z= 0.287 Chirality : 0.039 0.128 1989 Planarity : 0.004 0.048 2097 Dihedral : 10.664 123.085 1830 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.82 % Allowed : 12.75 % Favored : 85.43 % 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: 3.07 (0.21), residues: 1593 helix: 2.54 (0.14), residues: 1305 sheet: None (None), residues: 0 loop : -0.42 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 316 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 C 436 Details of bonding type rmsd hydrogen bonds : bond 0.06244 ( 979) hydrogen bonds : angle 4.10481 ( 2874) covalent geometry : bond 0.00512 (12744) covalent geometry : angle 0.53980 (17313) *********************** 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 182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7143 (mptt) cc_final: 0.6320 (tttt) REVERT: A 424 LEU cc_start: 0.8303 (tp) cc_final: 0.7943 (tm) REVERT: C 201 LYS cc_start: 0.6943 (mptt) cc_final: 0.6184 (tttt) REVERT: C 222 LEU cc_start: 0.8036 (tp) cc_final: 0.7352 (mt) REVERT: C 355 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7880 (ttt-90) REVERT: C 430 MET cc_start: 0.8535 (mtt) cc_final: 0.7936 (mtt) REVERT: C 489 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: C 592 ASP cc_start: 0.7688 (m-30) cc_final: 0.7400 (m-30) REVERT: B 222 LEU cc_start: 0.8087 (tt) cc_final: 0.7639 (mt) REVERT: B 267 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: B 305 MET cc_start: 0.8456 (mmp) cc_final: 0.8097 (mmt) REVERT: B 313 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8250 (mt) REVERT: B 424 LEU cc_start: 0.8384 (tp) cc_final: 0.8166 (tm) outliers start: 23 outliers final: 14 residues processed: 178 average time/residue: 2.0129 time to fit residues: 406.5236 Evaluate side-chains 175 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 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 620 ASN 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 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 83 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 123 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.0170 overall best weight: 1.1622 ------------------------------------------------------------------------------- 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 = 0.3579 r_free = 0.3579 target = 0.141827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.099037 restraints weight = 36576.795| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.27 r_work: 0.2936 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3716 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= 0.126 Angle : 0.462 5.849 17313 Z= 0.244 Chirality : 0.036 0.120 1989 Planarity : 0.003 0.043 2097 Dihedral : 10.030 117.587 1830 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.19 % Allowed : 13.46 % Favored : 85.35 % 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: 3.48 (0.21), residues: 1593 helix: 2.84 (0.14), residues: 1302 sheet: None (None), residues: 0 loop : -0.37 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 316 HIS 0.002 0.001 HIS C 288 PHE 0.014 0.001 PHE C 146 TYR 0.008 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 979) hydrogen bonds : angle 3.86880 ( 2874) covalent geometry : bond 0.00279 (12744) covalent geometry : angle 0.46161 (17313) ********************** 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 169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7168 (mptt) cc_final: 0.6402 (tttt) REVERT: A 242 GLN cc_start: 0.8669 (mt0) cc_final: 0.8405 (mt0) REVERT: C 201 LYS cc_start: 0.6934 (mptt) cc_final: 0.6187 (tttt) REVERT: C 222 LEU cc_start: 0.8004 (tp) cc_final: 0.7267 (mt) REVERT: C 242 GLN cc_start: 0.8780 (mt0) cc_final: 0.8346 (mt0) REVERT: C 355 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7793 (ttt-90) REVERT: C 430 MET cc_start: 0.8507 (mtt) cc_final: 0.7905 (mtt) REVERT: C 489 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: C 592 ASP cc_start: 0.7653 (m-30) cc_final: 0.7381 (m-30) REVERT: B 267 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: B 424 LEU cc_start: 0.8282 (tp) cc_final: 0.8059 (tm) outliers start: 15 outliers final: 11 residues processed: 165 average time/residue: 1.9615 time to fit residues: 362.2992 Evaluate side-chains 164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 119 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.143131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100559 restraints weight = 36388.194| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.27 r_work: 0.2958 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12744 Z= 0.110 Angle : 0.444 5.824 17313 Z= 0.233 Chirality : 0.035 0.118 1989 Planarity : 0.003 0.041 2097 Dihedral : 9.512 107.018 1830 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.19 % Allowed : 13.62 % Favored : 85.19 % 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: 3.75 (0.21), residues: 1593 helix: 3.08 (0.14), residues: 1290 sheet: None (None), residues: 0 loop : -0.37 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 316 HIS 0.002 0.000 HIS C 288 PHE 0.010 0.001 PHE C 279 TYR 0.008 0.001 TYR C 231 ARG 0.001 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 979) hydrogen bonds : angle 3.75328 ( 2874) covalent geometry : bond 0.00238 (12744) covalent geometry : angle 0.44358 (17313) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16484.86 seconds wall clock time: 285 minutes 17.19 seconds (17117.19 seconds total)