Starting phenix.real_space_refine on Thu Mar 13 14:29:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxa_24726/03_2025/7rxa_24726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxa_24726/03_2025/7rxa_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rxa_24726/03_2025/7rxa_24726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxa_24726/03_2025/7rxa_24726.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxa_24726/03_2025/7rxa_24726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxa_24726/03_2025/7rxa_24726.cif" } resolution = 3.08 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 18} 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, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 18} 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: 87 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: 87 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: 5.37, per 1000 atoms: 0.62 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.81 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: 2.30 Time building geometry restraints manager: 2.82 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: 4868 25.61 - 51.23: 220 51.23 - 76.84: 36 76.84 - 102.45: 12 102.45 - 128.07: 6 Dihedral angle restraints: 5142 sinusoidal: 1738 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=" O01 PGW B 903 " pdb=" C01 PGW B 903 " pdb=" C02 PGW B 903 " pdb=" O03 PGW B 903 " ideal model delta sinusoidal sigma weight residual 59.30 -52.04 111.34 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 5139 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: 0.04 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 724 or resid 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 C2 \ 2 or name C23 or name C24 or name C25 or name O01 or name O03 or name O04 or nam \ e O11 or name O12 or name O13 or name O14 or name P )) or (resid 904 and (name C \ 01 or name C02 or name C03 or name C06 or name C07 or name C1 or name C10 or nam \ e C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or na \ me 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: 1.270 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.290 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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= 0.424 Angle : 1.113 10.913 12156 Z= 0.544 Chirality : 0.048 0.177 1436 Planarity : 0.007 0.079 1484 Dihedral : 17.168 128.068 2922 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 (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: -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 TRP 0.017 0.001 TRP B 227 HIS 0.006 0.001 HIS A 619 PHE 0.016 0.002 PHE A 61 TYR 0.016 0.001 TYR B 589 ARG 0.004 0.000 ARG B 229 *********************** 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 : 0.887 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: 0.8399 (t80) cc_final: 0.8186 (t80) REVERT: B 428 LYS cc_start: 0.8172 (mttm) cc_final: 0.7935 (mttp) REVERT: B 551 ILE cc_start: 0.9078 (tt) cc_final: 0.8717 (tt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2303 time to fit residues: 35.4006 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 : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 280 GLN A 499 ASN A 518 GLN B 185 GLN B 280 GLN B 518 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098015 restraints weight = 11126.858| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.77 r_work: 0.2917 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8904 Z= 0.165 Angle : 0.520 6.764 12156 Z= 0.275 Chirality : 0.038 0.135 1436 Planarity : 0.005 0.059 1484 Dihedral : 14.961 123.686 1436 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.41 % Allowed : 9.32 % Favored : 90.27 % 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: -1.80 (0.23), residues: 1124 helix: -0.40 (0.18), residues: 788 sheet: -0.62 (0.53), residues: 40 loop : -3.29 (0.30), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 227 HIS 0.004 0.001 HIS B 619 PHE 0.018 0.001 PHE A 61 TYR 0.015 0.001 TYR B 589 ARG 0.002 0.000 ARG A 425 *********************** 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 107 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.903 Fit side-chains REVERT: A 355 GLN cc_start: 0.8276 (mm110) cc_final: 0.8028 (mm-40) REVERT: A 551 ILE cc_start: 0.8910 (tt) cc_final: 0.8567 (tt) REVERT: B 84 TRP cc_start: 0.7213 (t60) cc_final: 0.6983 (t60) REVERT: B 551 ILE cc_start: 0.9050 (tt) cc_final: 0.8701 (tt) outliers start: 3 outliers final: 3 residues processed: 107 average time/residue: 0.2032 time to fit residues: 32.7077 Evaluate side-chains 90 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 96 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.122675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.094194 restraints weight = 11392.785| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.79 r_work: 0.2864 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8904 Z= 0.274 Angle : 0.540 6.241 12156 Z= 0.284 Chirality : 0.040 0.144 1436 Planarity : 0.005 0.052 1484 Dihedral : 14.035 127.677 1436 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.49 % Allowed : 11.49 % Favored : 87.03 % 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: -0.72 (0.25), residues: 1124 helix: 0.47 (0.19), residues: 788 sheet: -0.87 (0.61), residues: 44 loop : -2.97 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 227 HIS 0.008 0.002 HIS B 619 PHE 0.024 0.001 PHE B 61 TYR 0.018 0.001 TYR A 589 ARG 0.002 0.000 ARG B 170 *********************** 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 113 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.890 Fit side-chains REVERT: A 84 TRP cc_start: 0.7217 (t60) cc_final: 0.6936 (t60) REVERT: A 335 MET cc_start: 0.8441 (ttm) cc_final: 0.8236 (mtp) REVERT: B 84 TRP cc_start: 0.7147 (t60) cc_final: 0.6920 (t60) REVERT: B 307 PHE cc_start: 0.8101 (t80) cc_final: 0.7853 (t80) outliers start: 11 outliers final: 9 residues processed: 109 average time/residue: 0.1617 time to fit residues: 26.6253 Evaluate side-chains 95 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 81 VAL Chi-restraints excluded: chain B residue 117 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.125616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.097265 restraints weight = 11257.207| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.79 r_work: 0.2901 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8904 Z= 0.161 Angle : 0.486 6.312 12156 Z= 0.255 Chirality : 0.038 0.128 1436 Planarity : 0.004 0.045 1484 Dihedral : 13.077 115.382 1436 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.62 % Allowed : 12.97 % Favored : 85.41 % 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: 0.04 (0.26), residues: 1124 helix: 1.05 (0.19), residues: 790 sheet: 0.10 (0.65), residues: 40 loop : -2.87 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.004 0.001 HIS B 619 PHE 0.017 0.001 PHE B 61 TYR 0.012 0.001 TYR A 589 ARG 0.001 0.000 ARG A 170 *********************** 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 111 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.905 Fit side-chains REVERT: A 84 TRP cc_start: 0.7106 (t60) cc_final: 0.6838 (t60) REVERT: A 117 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7613 (m) REVERT: B 84 TRP cc_start: 0.7071 (t60) cc_final: 0.6836 (t60) REVERT: B 117 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7637 (m) REVERT: B 551 ILE cc_start: 0.8930 (tt) cc_final: 0.8626 (tt) outliers start: 12 outliers final: 8 residues processed: 106 average time/residue: 0.1727 time to fit residues: 27.4536 Evaluate side-chains 98 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 555 CYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 136 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 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.124776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.096412 restraints weight = 11177.255| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.78 r_work: 0.2893 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1821 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= 0.198 Angle : 0.494 5.775 12156 Z= 0.259 Chirality : 0.039 0.135 1436 Planarity : 0.004 0.041 1484 Dihedral : 12.473 102.983 1436 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.49 % Allowed : 14.05 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.26), residues: 1124 helix: 1.34 (0.19), residues: 792 sheet: 0.16 (0.65), residues: 40 loop : -2.74 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.005 0.001 HIS A 619 PHE 0.018 0.001 PHE B 61 TYR 0.014 0.001 TYR A 589 ARG 0.001 0.000 ARG B 513 *********************** 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 111 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.907 Fit side-chains REVERT: A 84 TRP cc_start: 0.7155 (t60) cc_final: 0.6883 (t60) REVERT: A 117 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7672 (m) REVERT: A 551 ILE cc_start: 0.8918 (tt) cc_final: 0.8632 (tt) REVERT: B 84 TRP cc_start: 0.7107 (t60) cc_final: 0.6875 (t60) REVERT: B 117 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7699 (m) outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.1664 time to fit residues: 26.6182 Evaluate side-chains 98 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 THR Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain B residue 117 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 30 optimal weight: 0.0470 chunk 107 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.1280 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.123662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.095026 restraints weight = 11191.542| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.79 r_work: 0.2881 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1900 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= 0.228 Angle : 0.505 6.004 12156 Z= 0.264 Chirality : 0.039 0.138 1436 Planarity : 0.004 0.040 1484 Dihedral : 12.045 84.997 1436 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.03 % Allowed : 14.59 % Favored : 83.38 % 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: 0.60 (0.26), residues: 1124 helix: 1.49 (0.19), residues: 792 sheet: 0.01 (0.64), residues: 40 loop : -2.72 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.006 0.001 HIS B 619 PHE 0.018 0.001 PHE B 61 TYR 0.014 0.001 TYR B 589 ARG 0.001 0.000 ARG A 170 *********************** 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: 15 poor density : 96 time to evaluate : 0.975 Fit side-chains REVERT: A 84 TRP cc_start: 0.7197 (t60) cc_final: 0.6869 (t60) REVERT: A 531 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8651 (mp) REVERT: B 84 TRP cc_start: 0.7103 (t60) cc_final: 0.6861 (t60) REVERT: B 117 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7700 (m) REVERT: B 531 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8638 (mp) REVERT: B 551 ILE cc_start: 0.8946 (tt) cc_final: 0.8662 (tt) outliers start: 15 outliers final: 11 residues processed: 107 average time/residue: 0.1674 time to fit residues: 26.9562 Evaluate side-chains 101 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 334 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 555 CYS Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 117 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 85 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 0.0070 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.124079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.095351 restraints weight = 11277.504| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.80 r_work: 0.2902 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1974 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= 0.171 Angle : 0.482 5.679 12156 Z= 0.252 Chirality : 0.038 0.128 1436 Planarity : 0.004 0.038 1484 Dihedral : 11.266 81.641 1436 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.75 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 (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: 0.84 (0.26), residues: 1124 helix: 1.67 (0.19), residues: 800 sheet: 0.26 (0.64), residues: 40 loop : -2.79 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.004 0.001 HIS B 619 PHE 0.016 0.001 PHE B 61 TYR 0.012 0.001 TYR A 589 ARG 0.001 0.000 ARG B 237 *********************** 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 107 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.872 Fit side-chains REVERT: A 84 TRP cc_start: 0.7197 (t60) cc_final: 0.6830 (t60) REVERT: A 117 VAL cc_start: 0.7891 (OUTLIER) cc_final: 0.7639 (m) REVERT: A 531 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 551 ILE cc_start: 0.8895 (tt) cc_final: 0.8628 (tt) REVERT: B 84 TRP cc_start: 0.7150 (t60) cc_final: 0.6804 (t60) REVERT: B 117 VAL cc_start: 0.7859 (OUTLIER) cc_final: 0.7443 (m) REVERT: B 531 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8610 (mp) REVERT: B 551 ILE cc_start: 0.8923 (tt) cc_final: 0.8620 (tt) outliers start: 13 outliers final: 7 residues processed: 103 average time/residue: 0.1651 time to fit residues: 25.5249 Evaluate side-chains 99 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 117 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 109 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.126677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.098303 restraints weight = 11316.137| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.79 r_work: 0.2916 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8904 Z= 0.149 Angle : 0.473 5.825 12156 Z= 0.247 Chirality : 0.038 0.130 1436 Planarity : 0.004 0.036 1484 Dihedral : 10.938 83.256 1436 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.76 % Allowed : 15.14 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.26), residues: 1124 helix: 1.84 (0.19), residues: 800 sheet: 0.54 (0.67), residues: 40 loop : -2.76 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 227 HIS 0.004 0.001 HIS B 619 PHE 0.015 0.001 PHE B 61 TYR 0.012 0.001 TYR A 589 ARG 0.001 0.000 ARG A 170 *********************** 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 113 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.120 Fit side-chains REVERT: A 84 TRP cc_start: 0.7169 (t60) cc_final: 0.6811 (t60) REVERT: A 117 VAL cc_start: 0.7795 (OUTLIER) cc_final: 0.7384 (m) REVERT: A 158 LYS cc_start: 0.8393 (tttp) cc_final: 0.8088 (tttt) REVERT: A 531 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8614 (mp) REVERT: A 551 ILE cc_start: 0.8881 (tt) cc_final: 0.8592 (tt) REVERT: B 84 TRP cc_start: 0.7186 (t60) cc_final: 0.6871 (t60) REVERT: B 117 VAL cc_start: 0.7778 (OUTLIER) cc_final: 0.7357 (m) REVERT: B 531 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8603 (mp) REVERT: B 551 ILE cc_start: 0.8929 (tt) cc_final: 0.8626 (tt) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.2089 time to fit residues: 35.1418 Evaluate side-chains 106 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 117 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 109 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.123046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.094689 restraints weight = 11354.456| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.79 r_work: 0.2864 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8904 Z= 0.289 Angle : 0.533 5.776 12156 Z= 0.279 Chirality : 0.041 0.144 1436 Planarity : 0.004 0.037 1484 Dihedral : 11.224 81.706 1436 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.76 % Allowed : 15.14 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.26), residues: 1124 helix: 1.68 (0.19), residues: 800 sheet: 0.68 (0.72), residues: 40 loop : -2.78 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.008 0.001 HIS B 619 PHE 0.021 0.001 PHE B 61 TYR 0.016 0.001 TYR A 589 ARG 0.002 0.000 ARG B 513 *********************** 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 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.889 Fit side-chains REVERT: A 84 TRP cc_start: 0.7244 (t60) cc_final: 0.6892 (t60) REVERT: A 531 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8661 (mp) REVERT: A 551 ILE cc_start: 0.8927 (tt) cc_final: 0.8636 (tt) REVERT: B 84 TRP cc_start: 0.7228 (t60) cc_final: 0.6852 (t60) REVERT: B 117 VAL cc_start: 0.7984 (OUTLIER) cc_final: 0.7775 (m) REVERT: B 531 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 551 ILE cc_start: 0.8994 (tt) cc_final: 0.8704 (tt) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.1712 time to fit residues: 25.8482 Evaluate side-chains 97 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 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 81 VAL Chi-restraints excluded: chain B residue 117 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.123448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.095126 restraints weight = 11251.239| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.78 r_work: 0.2870 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8904 Z= 0.238 Angle : 0.513 5.921 12156 Z= 0.270 Chirality : 0.040 0.138 1436 Planarity : 0.004 0.038 1484 Dihedral : 11.248 84.305 1436 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.76 % Allowed : 15.14 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.26), residues: 1124 helix: 1.73 (0.19), residues: 800 sheet: 0.74 (0.75), residues: 40 loop : -2.74 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.006 0.001 HIS B 619 PHE 0.018 0.001 PHE B 61 TYR 0.014 0.001 TYR B 589 ARG 0.001 0.000 ARG B 170 ********************** 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 98 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 1.030 Fit side-chains REVERT: A 84 TRP cc_start: 0.7203 (t60) cc_final: 0.6846 (t60) REVERT: A 531 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8636 (mp) REVERT: A 551 ILE cc_start: 0.8925 (tt) cc_final: 0.8634 (tt) REVERT: B 84 TRP cc_start: 0.7259 (t60) cc_final: 0.6903 (t60) REVERT: B 117 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7742 (m) REVERT: B 531 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8654 (mp) REVERT: B 551 ILE cc_start: 0.8962 (tt) cc_final: 0.8655 (tt) outliers start: 13 outliers final: 10 residues processed: 95 average time/residue: 0.1742 time to fit residues: 24.6758 Evaluate side-chains 96 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 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 81 VAL Chi-restraints excluded: chain B residue 117 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 41 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.122738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.094477 restraints weight = 11252.905| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.78 r_work: 0.2863 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8904 Z= 0.285 Angle : 0.535 6.071 12156 Z= 0.281 Chirality : 0.041 0.144 1436 Planarity : 0.004 0.038 1484 Dihedral : 11.446 86.179 1436 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.89 % Allowed : 15.27 % Favored : 82.84 % 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: 0.90 (0.26), residues: 1124 helix: 1.69 (0.19), residues: 800 sheet: 0.74 (0.76), residues: 40 loop : -2.74 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.007 0.001 HIS B 619 PHE 0.020 0.001 PHE B 61 TYR 0.015 0.001 TYR B 589 ARG 0.002 0.000 ARG B 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4402.70 seconds wall clock time: 77 minutes 22.09 seconds (4642.09 seconds total)