Starting phenix.real_space_refine on Thu Jul 2 14:13:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rxa_24726/07_2026/7rxa_24726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxa_24726/07_2026/7rxa_24726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rxa_24726/07_2026/7rxa_24726.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rxa_24726/07_2026/7rxa_24726.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rxa_24726/07_2026/7rxa_24726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxa_24726/07_2026/7rxa_24726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rxa_24726/07_2026/7rxa_24726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxa_24726/07_2026/7rxa_24726.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 30 5.16 5 C 5770 2.51 5 N 1418 2.21 5 O 1468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8694 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4221 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 23, 'TRANS': 554} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 675 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 35, 'ASP:plan': 17, 'ASN:plan1': 6, 'ARG:plan': 18, 'HIS:plan': 2, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 366 Chain: "B" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4221 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 23, 'TRANS': 554} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 675 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 35, 'ASP:plan': 17, 'ASN:plan1': 6, 'ARG:plan': 18, 'HIS:plan': 2, 'PHE:plan': 2, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 366 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 1.99, per 1000 atoms: 0.23 Number of scatterers: 8694 At special positions: 0 Unit cell: (71.02, 119.78, 96.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 8 15.00 O 1468 8.00 N 1418 7.00 C 5770 6.00 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: 0.76 Conformation dependent library (CDL) restraints added in 219.7 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 72.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 31 through 46 removed outlier: 3.534A pdb=" N GLU A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 86 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.658A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 191 removed outlier: 4.164A pdb=" N VAL A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 4.008A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 238 removed outlier: 3.743A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.807A pdb=" N TYR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 311 removed outlier: 3.514A pdb=" N PHE A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.760A pdb=" N ALA A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 375 removed outlier: 4.283A pdb=" N VAL A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.866A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 422 through 442 removed outlier: 4.148A pdb=" N LEU A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLN A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 507 through 525 removed outlier: 4.424A pdb=" N ALA A 511 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 519 " --> pdb=" O MET A 515 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 529 Processing helix chain 'A' and resid 531 through 543 removed outlier: 3.513A pdb=" N ASN A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 554 Processing helix chain 'A' and resid 568 through 592 removed outlier: 3.647A pdb=" N SER A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 635 removed outlier: 3.587A pdb=" N LEU A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 659 removed outlier: 3.920A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 654 " --> pdb=" O MET A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 3.752A pdb=" N MET A 707 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A 708 " --> pdb=" O PHE A 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 704 through 708' Processing helix chain 'A' and resid 712 through 724 removed outlier: 3.813A pdb=" N THR A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 46 removed outlier: 3.534A pdb=" N GLU B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 162 through 172 removed outlier: 3.658A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 191 removed outlier: 4.164A pdb=" N VAL B 177 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 4.008A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 238 removed outlier: 3.743A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.807A pdb=" N TYR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 311 removed outlier: 3.515A pdb=" N PHE B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 322 through 331 Processing helix chain 'B' and resid 331 through 350 removed outlier: 3.761A pdb=" N ALA B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 338 " --> pdb=" O THR B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 375 removed outlier: 4.283A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.866A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 422 through 442 removed outlier: 4.147A pdb=" N LEU B 426 " --> pdb=" O ASN B 422 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLN B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 501 Processing helix chain 'B' and resid 507 through 525 removed outlier: 4.424A pdb=" N ALA B 511 " --> pdb=" O ASP B 507 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG B 513 " --> pdb=" O THR B 509 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 519 " --> pdb=" O MET B 515 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 529 Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.514A pdb=" N ASN B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 554 Processing helix chain 'B' and resid 568 through 592 removed outlier: 3.646A pdb=" N SER B 572 " --> pdb=" O PRO B 568 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 635 removed outlier: 3.587A pdb=" N LEU B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 659 removed outlier: 3.921A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 654 " --> pdb=" O MET B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 removed outlier: 3.752A pdb=" N MET B 707 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG B 708 " --> pdb=" O PHE B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 708' Processing helix chain 'B' and resid 712 through 724 removed outlier: 3.814A pdb=" N THR B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 56 removed outlier: 6.374A pdb=" N SER A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A 19 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE A 139 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ARG A 21 " --> pdb=" O ASP A 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 56 removed outlier: 6.375A pdb=" N SER B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 19 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ILE B 139 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG B 21 " --> pdb=" O ASP B 137 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1268 1.31 - 1.43: 2622 1.43 - 1.56: 4958 1.56 - 1.69: 16 1.69 - 1.81: 40 Bond restraints: 8904 Sorted by residual: bond pdb=" C1 PGW A 801 " pdb=" O01 PGW A 801 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 PGW B 904 " pdb=" O01 PGW B 904 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 PGW A 804 " pdb=" O01 PGW A 804 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 PGW B 903 " pdb=" O01 PGW B 903 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 PGW B 901 " pdb=" O01 PGW B 901 " ideal model delta sigma weight residual 1.332 1.419 -0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 11599 2.18 - 4.37: 407 4.37 - 6.55: 86 6.55 - 8.73: 40 8.73 - 10.91: 24 Bond angle restraints: 12156 Sorted by residual: angle pdb=" N GLU A 154 " pdb=" CA GLU A 154 " pdb=" C GLU A 154 " ideal model delta sigma weight residual 114.64 107.25 7.39 1.52e+00 4.33e-01 2.37e+01 angle pdb=" N GLU B 154 " pdb=" CA GLU B 154 " pdb=" C GLU B 154 " ideal model delta sigma weight residual 114.64 107.26 7.38 1.52e+00 4.33e-01 2.36e+01 angle pdb=" C LYS B 158 " pdb=" N THR B 159 " pdb=" CA THR B 159 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C LYS A 158 " pdb=" N THR A 159 " pdb=" CA THR A 159 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N ILE B 605 " pdb=" CA ILE B 605 " pdb=" C ILE B 605 " ideal model delta sigma weight residual 113.71 109.85 3.86 9.50e-01 1.11e+00 1.65e+01 ... (remaining 12151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 4860 25.61 - 51.23: 192 51.23 - 76.84: 26 76.84 - 102.45: 4 102.45 - 128.07: 2 Dihedral angle restraints: 5084 sinusoidal: 1680 harmonic: 3404 Sorted by residual: dihedral pdb=" C15 PGW B 904 " pdb=" C16 PGW B 904 " pdb=" C17 PGW B 904 " pdb=" C18 PGW B 904 " ideal model delta sinusoidal sigma weight residual 178.71 -53.22 -128.07 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C15 PGW A 801 " pdb=" C16 PGW A 801 " pdb=" C17 PGW A 801 " pdb=" C18 PGW A 801 " ideal model delta sinusoidal sigma weight residual 178.71 -53.23 -128.06 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" CA THR B 127 " pdb=" C THR B 127 " pdb=" N PRO B 128 " pdb=" CA PRO B 128 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 5081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 861 0.036 - 0.071: 381 0.071 - 0.106: 134 0.106 - 0.142: 48 0.142 - 0.177: 12 Chirality restraints: 1436 Sorted by residual: chirality pdb=" C02 PGW A 802 " pdb=" C01 PGW A 802 " pdb=" C03 PGW A 802 " pdb=" O01 PGW A 802 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" C02 PGW B 901 " pdb=" C01 PGW B 901 " pdb=" C03 PGW B 901 " pdb=" O01 PGW B 901 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA PRO A 128 " pdb=" N PRO A 128 " pdb=" C PRO A 128 " pdb=" CB PRO A 128 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 1433 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 376 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 377 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 377 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 377 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 376 " 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 377 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 422 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO B 423 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.040 5.00e-02 4.00e+02 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3234 2.89 - 3.39: 7907 3.39 - 3.89: 14203 3.89 - 4.40: 15720 4.40 - 4.90: 27731 Nonbonded interactions: 68795 Sorted by model distance: nonbonded pdb=" O GLY A 580 " pdb=" OG SER A 584 " model vdw 2.381 3.040 nonbonded pdb=" O GLY B 580 " pdb=" OG SER B 584 " model vdw 2.381 3.040 nonbonded pdb=" NE1 TRP B 155 " pdb=" OD1 ASP B 165 " model vdw 2.420 3.120 nonbonded pdb=" NE1 TRP A 155 " pdb=" OD1 ASP A 165 " model vdw 2.420 3.120 nonbonded pdb=" O SER A 374 " pdb=" OH TYR A 521 " model vdw 2.444 3.040 ... (remaining 68790 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 724 or (resid 801 and (name C01 or name C02 or \ name C03 or name C06 or name C1 or name C10 or name C15 or name C19 or name C2 o \ r name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 \ or name C9 or name O01 or name O02 or name O03 or name O04 or name O11 or name \ O12 or name O13 or name O14 or name P )) or (resid 802 through 803 and (name C01 \ or name C02 or name C03 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name O01 or name O03 or name O04 or name O11 or \ name O12 or name O13 or name O14 or name P )) or resid 804)) selection = (chain 'B' and (resid 11 through 901 or (resid 902 through 903 and (name C01 or \ name C02 or name C03 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name O01 or name O03 or name O04 or name O11 or name \ O12 or name O13 or name O14 or name P )) or (resid 904 and (name C01 or name C0 \ 2 or name C03 or name C06 or name C07 or name C1 or name C10 or name C19 or name \ C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or n \ ame C3 or name C4 or name C5 or name C6 or name C7 or name C8 or name C9 or name \ O01 or name O02 or name O03 or name O04 or name O11 or name O12 or name O13 or \ name O14 or name P )))) } 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 : 0.006 0.090 8904 Z= 0.312 Angle : 1.113 10.913 12156 Z= 0.544 Chirality : 0.048 0.177 1436 Planarity : 0.007 0.079 1484 Dihedral : 15.073 128.068 2864 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.42 (0.18), residues: 1124 helix: -2.49 (0.13), residues: 780 sheet: -1.78 (0.57), residues: 44 loop : -3.79 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 229 TYR 0.016 0.001 TYR B 589 PHE 0.016 0.002 PHE A 61 TRP 0.017 0.001 TRP B 227 HIS 0.006 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.31 ( 8904) covalent geometry : angle 1.11314 / 0.54 (12156) hydrogen bonds : bond 0.16526 / 11.35 ( 556) hydrogen bonds : angle 6.60599 / 4.54 ( 1656) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.320 Fit side-chains REVERT: A 14 HIS cc_start: 0.8219 (m-70) cc_final: 0.7971 (m90) REVERT: A 355 GLN cc_start: 0.8075 (mm110) cc_final: 0.7838 (mm-40) REVERT: A 428 LYS cc_start: 0.8167 (mttm) cc_final: 0.7966 (mttp) REVERT: A 626 TYR cc_start: 0.8400 (t80) cc_final: 0.8186 (t80) REVERT: B 428 LYS cc_start: 0.8171 (mttm) cc_final: 0.7935 (mttp) REVERT: B 551 ILE cc_start: 0.9078 (tt) cc_final: 0.8716 (tt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.0829 time to fit residues: 12.8786 Evaluate side-chains 82 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.0170 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.0470 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 GLN A 499 ASN A 518 GLN B 185 GLN B 518 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098639 restraints weight = 11210.202| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.79 r_work: 0.2936 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8904 Z= 0.102 Angle : 0.510 6.853 12156 Z= 0.271 Chirality : 0.037 0.129 1436 Planarity : 0.005 0.059 1484 Dihedral : 11.673 120.396 1378 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.41 % Allowed : 9.19 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.23), residues: 1124 helix: -0.45 (0.17), residues: 788 sheet: -1.08 (0.55), residues: 44 loop : -3.32 (0.30), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 425 TYR 0.013 0.001 TYR A 589 PHE 0.016 0.001 PHE A 61 TRP 0.011 0.001 TRP B 227 HIS 0.003 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 ( 8904) covalent geometry : angle 0.50987 / 0.27 (12156) hydrogen bonds : bond 0.03631 / 2.51 ( 556) hydrogen bonds : angle 4.26634 / 2.98 ( 1656) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.213 Fit side-chains REVERT: A 355 GLN cc_start: 0.8287 (mm110) cc_final: 0.8042 (mm-40) REVERT: A 551 ILE cc_start: 0.8880 (tt) cc_final: 0.8537 (tt) REVERT: B 551 ILE cc_start: 0.9045 (tt) cc_final: 0.8700 (tt) outliers start: 3 outliers final: 3 residues processed: 112 average time/residue: 0.0619 time to fit residues: 10.2483 Evaluate side-chains 89 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 658 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.093896 restraints weight = 11297.054| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.78 r_work: 0.2865 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8904 Z= 0.193 Angle : 0.554 6.278 12156 Z= 0.291 Chirality : 0.041 0.144 1436 Planarity : 0.005 0.052 1484 Dihedral : 10.750 124.829 1378 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.76 % Allowed : 10.68 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.25), residues: 1124 helix: 0.42 (0.19), residues: 788 sheet: -0.38 (0.58), residues: 40 loop : -3.04 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 170 TYR 0.018 0.001 TYR A 589 PHE 0.025 0.002 PHE A 61 TRP 0.014 0.001 TRP A 227 HIS 0.008 0.002 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.19 ( 8904) covalent geometry : angle 0.55365 / 0.29 (12156) hydrogen bonds : bond 0.03732 / 2.61 ( 556) hydrogen bonds : angle 4.02124 / 2.82 ( 1656) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.209 Fit side-chains REVERT: A 355 GLN cc_start: 0.8293 (mm110) cc_final: 0.8011 (mm-40) REVERT: A 626 TYR cc_start: 0.8943 (t80) cc_final: 0.8742 (t80) REVERT: B 307 PHE cc_start: 0.8114 (t80) cc_final: 0.7869 (t80) REVERT: B 551 ILE cc_start: 0.9118 (tt) cc_final: 0.8768 (tt) outliers start: 13 outliers final: 11 residues processed: 105 average time/residue: 0.0667 time to fit residues: 10.6003 Evaluate side-chains 95 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 0.0370 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.125489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097012 restraints weight = 11351.920| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.81 r_work: 0.2900 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8904 Z= 0.112 Angle : 0.487 6.256 12156 Z= 0.256 Chirality : 0.038 0.128 1436 Planarity : 0.004 0.045 1484 Dihedral : 9.921 113.314 1378 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.49 % Allowed : 12.70 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.26), residues: 1124 helix: 1.01 (0.19), residues: 788 sheet: -0.04 (0.63), residues: 40 loop : -2.93 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 170 TYR 0.012 0.001 TYR A 589 PHE 0.018 0.001 PHE A 61 TRP 0.013 0.001 TRP B 84 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8904) covalent geometry : angle 0.48666 / 0.26 (12156) hydrogen bonds : bond 0.03101 / 2.16 ( 556) hydrogen bonds : angle 3.82165 / 2.68 ( 1656) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.195 Fit side-chains REVERT: A 84 TRP cc_start: 0.7134 (t60) cc_final: 0.6870 (t60) REVERT: A 355 GLN cc_start: 0.8215 (mm110) cc_final: 0.7939 (mm-40) REVERT: A 551 ILE cc_start: 0.8914 (tt) cc_final: 0.8617 (tt) REVERT: B 551 ILE cc_start: 0.9071 (tt) cc_final: 0.8715 (tt) outliers start: 11 outliers final: 9 residues processed: 105 average time/residue: 0.0641 time to fit residues: 10.2411 Evaluate side-chains 93 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097034 restraints weight = 11295.400| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.79 r_work: 0.2903 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8904 Z= 0.116 Angle : 0.487 5.840 12156 Z= 0.255 Chirality : 0.038 0.131 1436 Planarity : 0.004 0.040 1484 Dihedral : 9.243 98.795 1378 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.62 % Allowed : 13.38 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1124 helix: 1.31 (0.19), residues: 792 sheet: 0.27 (0.66), residues: 40 loop : -2.76 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 237 TYR 0.013 0.001 TYR A 589 PHE 0.018 0.001 PHE B 61 TRP 0.012 0.001 TRP B 84 HIS 0.005 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 8904) covalent geometry : angle 0.48694 / 0.26 (12156) hydrogen bonds : bond 0.03099 / 2.17 ( 556) hydrogen bonds : angle 3.74016 / 2.63 ( 1656) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.206 Fit side-chains REVERT: A 84 TRP cc_start: 0.7138 (t60) cc_final: 0.6866 (t60) REVERT: A 117 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7642 (m) REVERT: A 355 GLN cc_start: 0.8198 (mm110) cc_final: 0.7916 (mm-40) REVERT: B 551 ILE cc_start: 0.9064 (tt) cc_final: 0.8700 (tt) outliers start: 12 outliers final: 9 residues processed: 107 average time/residue: 0.0665 time to fit residues: 10.7905 Evaluate side-chains 97 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 0.0570 chunk 44 optimal weight: 0.0010 chunk 77 optimal weight: 1.9990 overall best weight: 0.7906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.097196 restraints weight = 11221.463| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.79 r_work: 0.2900 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8904 Z= 0.115 Angle : 0.484 5.961 12156 Z= 0.254 Chirality : 0.038 0.132 1436 Planarity : 0.004 0.038 1484 Dihedral : 8.411 69.407 1378 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.89 % Allowed : 14.32 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.26), residues: 1124 helix: 1.55 (0.19), residues: 792 sheet: 0.47 (0.66), residues: 40 loop : -2.75 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 513 TYR 0.013 0.001 TYR A 589 PHE 0.017 0.001 PHE B 61 TRP 0.011 0.001 TRP B 84 HIS 0.004 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 8904) covalent geometry : angle 0.48439 / 0.25 (12156) hydrogen bonds : bond 0.03068 / 2.15 ( 556) hydrogen bonds : angle 3.71425 / 2.61 ( 1656) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.320 Fit side-chains REVERT: A 84 TRP cc_start: 0.7115 (t60) cc_final: 0.6851 (t60) REVERT: A 117 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7544 (m) REVERT: A 531 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 551 ILE cc_start: 0.8897 (tt) cc_final: 0.8621 (tt) REVERT: B 531 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8610 (mp) REVERT: B 551 ILE cc_start: 0.9057 (tt) cc_final: 0.8692 (tt) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.0645 time to fit residues: 10.3782 Evaluate side-chains 101 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.0870 chunk 84 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.096360 restraints weight = 11327.746| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.80 r_work: 0.2889 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8904 Z= 0.132 Angle : 0.492 5.763 12156 Z= 0.259 Chirality : 0.039 0.134 1436 Planarity : 0.004 0.037 1484 Dihedral : 8.157 56.800 1378 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.03 % Allowed : 13.92 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1124 helix: 1.63 (0.19), residues: 792 sheet: 0.46 (0.64), residues: 40 loop : -2.71 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.014 0.001 TYR A 589 PHE 0.018 0.001 PHE A 61 TRP 0.011 0.001 TRP B 84 HIS 0.006 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 ( 8904) covalent geometry : angle 0.49224 / 0.26 (12156) hydrogen bonds : bond 0.03149 / 2.21 ( 556) hydrogen bonds : angle 3.70828 / 2.61 ( 1656) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.272 Fit side-chains REVERT: A 84 TRP cc_start: 0.7090 (t60) cc_final: 0.6826 (t60) REVERT: A 117 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7644 (m) REVERT: A 531 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8616 (mp) REVERT: A 551 ILE cc_start: 0.8923 (tt) cc_final: 0.8625 (tt) REVERT: B 531 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8633 (mp) outliers start: 15 outliers final: 10 residues processed: 107 average time/residue: 0.0632 time to fit residues: 10.1931 Evaluate side-chains 100 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 555 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 0.0270 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.126186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097675 restraints weight = 11152.721| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.78 r_work: 0.2909 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8904 Z= 0.111 Angle : 0.478 5.740 12156 Z= 0.251 Chirality : 0.038 0.131 1436 Planarity : 0.004 0.037 1484 Dihedral : 7.909 57.536 1378 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.03 % Allowed : 14.19 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1124 helix: 1.78 (0.19), residues: 792 sheet: 0.59 (0.65), residues: 40 loop : -2.71 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 170 TYR 0.012 0.001 TYR A 589 PHE 0.022 0.001 PHE A 307 TRP 0.011 0.001 TRP B 227 HIS 0.004 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 8904) covalent geometry : angle 0.47816 / 0.25 (12156) hydrogen bonds : bond 0.03001 / 2.10 ( 556) hydrogen bonds : angle 3.69980 / 2.61 ( 1656) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.318 Fit side-chains REVERT: A 84 TRP cc_start: 0.7227 (t60) cc_final: 0.6855 (t60) REVERT: A 117 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7535 (m) REVERT: A 531 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8628 (mp) REVERT: A 551 ILE cc_start: 0.8937 (tt) cc_final: 0.8638 (tt) REVERT: B 531 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8622 (mp) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.0614 time to fit residues: 9.9784 Evaluate side-chains 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 555 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 11 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.097562 restraints weight = 11173.362| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.79 r_work: 0.2907 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8904 Z= 0.116 Angle : 0.485 5.701 12156 Z= 0.254 Chirality : 0.039 0.131 1436 Planarity : 0.004 0.036 1484 Dihedral : 7.775 58.170 1378 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.76 % Allowed : 14.59 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1124 helix: 1.85 (0.19), residues: 792 sheet: 0.78 (0.70), residues: 40 loop : -2.71 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 170 TYR 0.013 0.001 TYR B 589 PHE 0.020 0.001 PHE A 307 TRP 0.014 0.001 TRP B 84 HIS 0.005 0.001 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8904) covalent geometry : angle 0.48503 / 0.25 (12156) hydrogen bonds : bond 0.03013 / 2.11 ( 556) hydrogen bonds : angle 3.66625 / 2.58 ( 1656) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.257 Fit side-chains REVERT: A 84 TRP cc_start: 0.7233 (t60) cc_final: 0.6862 (t60) REVERT: A 117 VAL cc_start: 0.7864 (OUTLIER) cc_final: 0.7451 (m) REVERT: A 158 LYS cc_start: 0.8387 (tttp) cc_final: 0.8065 (tttt) REVERT: A 531 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8631 (mp) REVERT: A 551 ILE cc_start: 0.8938 (tt) cc_final: 0.8643 (tt) REVERT: B 531 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8627 (mp) outliers start: 13 outliers final: 10 residues processed: 103 average time/residue: 0.0702 time to fit residues: 11.0234 Evaluate side-chains 102 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098052 restraints weight = 11182.051| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.80 r_work: 0.2913 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8904 Z= 0.108 Angle : 0.480 5.782 12156 Z= 0.252 Chirality : 0.038 0.129 1436 Planarity : 0.004 0.036 1484 Dihedral : 7.619 59.191 1378 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.03 % Allowed : 13.78 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.26), residues: 1124 helix: 1.93 (0.19), residues: 792 sheet: 0.97 (0.75), residues: 40 loop : -2.70 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 170 TYR 0.012 0.001 TYR A 589 PHE 0.020 0.001 PHE A 307 TRP 0.013 0.001 TRP B 84 HIS 0.004 0.001 HIS B 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 8904) covalent geometry : angle 0.48046 / 0.25 (12156) hydrogen bonds : bond 0.02964 / 2.08 ( 556) hydrogen bonds : angle 3.64192 / 2.56 ( 1656) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.324 Fit side-chains REVERT: A 84 TRP cc_start: 0.7222 (t60) cc_final: 0.6863 (t60) REVERT: A 117 VAL cc_start: 0.7793 (OUTLIER) cc_final: 0.7384 (m) REVERT: A 158 LYS cc_start: 0.8361 (tttp) cc_final: 0.8055 (tttt) REVERT: A 531 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8625 (mp) REVERT: A 551 ILE cc_start: 0.8935 (tt) cc_final: 0.8640 (tt) REVERT: B 531 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8625 (mp) REVERT: B 551 ILE cc_start: 0.8881 (tt) cc_final: 0.8581 (tt) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.0697 time to fit residues: 10.9654 Evaluate side-chains 103 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 555 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 40 optimal weight: 0.0060 chunk 86 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 96 optimal weight: 0.5980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.101109 restraints weight = 11077.357| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.79 r_work: 0.2960 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8904 Z= 0.088 Angle : 0.460 5.591 12156 Z= 0.240 Chirality : 0.037 0.120 1436 Planarity : 0.004 0.036 1484 Dihedral : 7.018 58.274 1378 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.95 % Allowed : 15.27 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.26), residues: 1124 helix: 2.03 (0.19), residues: 806 sheet: 1.02 (0.74), residues: 40 loop : -2.82 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 237 TYR 0.010 0.001 TYR B 589 PHE 0.019 0.001 PHE A 307 TRP 0.012 0.001 TRP B 84 HIS 0.003 0.000 HIS A 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 ( 8904) covalent geometry : angle 0.45986 / 0.24 (12156) hydrogen bonds : bond 0.02682 / 1.88 ( 556) hydrogen bonds : angle 3.54767 / 2.50 ( 1656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.72 seconds wall clock time: 33 minutes 2.05 seconds (1982.05 seconds total)