Starting phenix.real_space_refine on Thu Feb 13 12:02:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxa_24726/02_2025/7rxa_24726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxa_24726/02_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_24726/02_2025/7rxa_24726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxa_24726/02_2025/7rxa_24726.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxa_24726/02_2025/7rxa_24726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxa_24726/02_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-5592/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: 5.39, 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 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: 2.55 Time building geometry restraints manager: 2.58 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: 0.05 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: 1.220 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.250 Find NCS groups from input model: 0.390 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- 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 : 1.040 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: 0.2296 time to fit residues: 35.1856 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 : 0.968 ------------------------------------------------------------------------------- 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 = 0.126147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098027 restraints weight = 11120.809| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.77 r_work: 0.2910 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 6.763 12156 Z= 0.275 Chirality : 0.038 0.135 1436 Planarity : 0.005 0.059 1484 Dihedral : 14.965 123.699 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 : 0.995 Fit side-chains REVERT: A 355 GLN cc_start: 0.8262 (mm110) cc_final: 0.8003 (mm-40) REVERT: A 551 ILE cc_start: 0.8877 (tt) cc_final: 0.8537 (tt) REVERT: B 84 TRP cc_start: 0.7166 (t60) cc_final: 0.6936 (t60) REVERT: B 551 ILE cc_start: 0.9019 (tt) cc_final: 0.8674 (tt) outliers start: 3 outliers final: 3 residues processed: 107 average time/residue: 0.1759 time to fit residues: 27.9577 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 : 0.977 ------------------------------------------------------------------------------- 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: 0.3980 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.125689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097351 restraints weight = 11293.654| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.79 r_work: 0.2903 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8904 Z= 0.180 Angle : 0.495 5.971 12156 Z= 0.260 Chirality : 0.038 0.133 1436 Planarity : 0.004 0.047 1484 Dihedral : 13.690 119.006 1436 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.49 % Allowed : 10.68 % Favored : 87.84 % 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: -0.55 (0.25), residues: 1124 helix: 0.61 (0.19), residues: 788 sheet: -0.16 (0.59), residues: 40 loop : -3.05 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.005 0.001 HIS B 619 PHE 0.021 0.001 PHE B 61 TYR 0.015 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 : 0.909 Fit side-chains REVERT: A 84 TRP cc_start: 0.7155 (t60) cc_final: 0.6862 (t60) REVERT: A 355 GLN cc_start: 0.8247 (mm110) cc_final: 0.7969 (mm-40) REVERT: A 551 ILE cc_start: 0.8932 (tt) cc_final: 0.8583 (tt) REVERT: B 84 TRP cc_start: 0.7213 (t60) cc_final: 0.6951 (t60) REVERT: B 117 VAL cc_start: 0.7932 (OUTLIER) cc_final: 0.7720 (m) REVERT: B 307 PHE cc_start: 0.8061 (t80) cc_final: 0.7784 (t80) REVERT: B 551 ILE cc_start: 0.9067 (tt) cc_final: 0.8713 (tt) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.1671 time to fit residues: 27.2791 Evaluate side-chains 99 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.0070 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 = 0.126971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.098868 restraints weight = 11190.916| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.78 r_work: 0.2924 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8904 Z= 0.145 Angle : 0.477 6.077 12156 Z= 0.249 Chirality : 0.038 0.127 1436 Planarity : 0.004 0.041 1484 Dihedral : 12.548 98.894 1436 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.08 % Allowed : 12.43 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1124 helix: 1.17 (0.19), residues: 790 sheet: 0.10 (0.63), residues: 40 loop : -2.86 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.003 0.001 HIS A 619 PHE 0.015 0.001 PHE B 61 TYR 0.012 0.001 TYR A 589 ARG 0.001 0.000 ARG A 237 *********************** 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 109 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 1.229 Fit side-chains REVERT: A 84 TRP cc_start: 0.7112 (t60) cc_final: 0.6835 (t60) REVERT: A 355 GLN cc_start: 0.8171 (mm110) cc_final: 0.7898 (mm-40) REVERT: A 551 ILE cc_start: 0.8910 (tt) cc_final: 0.8589 (tt) REVERT: B 84 TRP cc_start: 0.7108 (t60) cc_final: 0.6872 (t60) REVERT: B 117 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7326 (m) REVERT: B 500 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8252 (tt0) REVERT: B 551 ILE cc_start: 0.9022 (tt) cc_final: 0.8654 (tt) outliers start: 8 outliers final: 6 residues processed: 106 average time/residue: 0.1780 time to fit residues: 28.4523 Evaluate side-chains 97 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 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 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: 1.9990 chunk 107 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.0570 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.126120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097754 restraints weight = 11115.653| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.79 r_work: 0.2858 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1855 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= 0.160 Angle : 0.477 5.789 12156 Z= 0.250 Chirality : 0.038 0.134 1436 Planarity : 0.004 0.038 1484 Dihedral : 11.651 86.498 1436 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.62 % Allowed : 13.51 % Favored : 84.86 % 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: 0.57 (0.26), residues: 1124 helix: 1.48 (0.19), residues: 792 sheet: -0.43 (0.65), residues: 44 loop : -2.70 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 227 HIS 0.004 0.001 HIS A 619 PHE 0.016 0.001 PHE B 61 TYR 0.013 0.001 TYR B 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: 12 poor density : 99 time to evaluate : 0.896 Fit side-chains REVERT: A 84 TRP cc_start: 0.7020 (t60) cc_final: 0.6731 (t60) REVERT: A 551 ILE cc_start: 0.8855 (tt) cc_final: 0.8539 (tt) REVERT: B 84 TRP cc_start: 0.6978 (t60) cc_final: 0.6713 (t60) REVERT: B 117 VAL cc_start: 0.7758 (OUTLIER) cc_final: 0.7338 (m) REVERT: B 551 ILE cc_start: 0.8968 (tt) cc_final: 0.8607 (tt) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.1691 time to fit residues: 27.3331 Evaluate side-chains 102 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 107 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 60 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 HIS B 619 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.127841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099709 restraints weight = 11070.819| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.79 r_work: 0.2938 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1986 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= 0.138 Angle : 0.466 5.977 12156 Z= 0.243 Chirality : 0.038 0.128 1436 Planarity : 0.004 0.037 1484 Dihedral : 11.307 89.366 1436 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.35 % Allowed : 14.05 % Favored : 84.59 % 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: 0.82 (0.26), residues: 1124 helix: 1.71 (0.19), residues: 796 sheet: -0.31 (0.63), residues: 44 loop : -2.84 (0.33), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 227 HIS 0.003 0.001 HIS A 619 PHE 0.014 0.001 PHE B 61 TYR 0.012 0.001 TYR A 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 112 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.985 Fit side-chains REVERT: A 84 TRP cc_start: 0.7068 (t60) cc_final: 0.6809 (t60) REVERT: A 551 ILE cc_start: 0.8935 (tt) cc_final: 0.8600 (tt) REVERT: B 84 TRP cc_start: 0.7035 (t60) cc_final: 0.6779 (t60) REVERT: B 117 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7332 (m) REVERT: B 551 ILE cc_start: 0.9021 (tt) cc_final: 0.8653 (tt) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 0.1658 time to fit residues: 26.9674 Evaluate side-chains 102 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 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 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: 4.9990 chunk 21 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.125015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096759 restraints weight = 11263.768| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.78 r_work: 0.2880 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8904 Z= 0.222 Angle : 0.502 5.652 12156 Z= 0.263 Chirality : 0.039 0.142 1436 Planarity : 0.004 0.036 1484 Dihedral : 11.271 88.472 1436 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.35 % Allowed : 14.05 % Favored : 84.59 % 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: 1.74 (0.19), residues: 792 sheet: -0.27 (0.64), residues: 44 loop : -2.66 (0.34), residues: 288 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 0.018 0.001 PHE B 61 TYR 0.015 0.001 TYR A 589 ARG 0.001 0.000 ARG A 513 *********************** 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 108 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.085 Fit side-chains REVERT: A 84 TRP cc_start: 0.7069 (t60) cc_final: 0.6785 (t60) REVERT: B 84 TRP cc_start: 0.7036 (t60) cc_final: 0.6800 (t60) REVERT: B 117 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7377 (m) outliers start: 10 outliers final: 8 residues processed: 106 average time/residue: 0.1918 time to fit residues: 30.2505 Evaluate side-chains 98 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 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 555 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.125803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097331 restraints weight = 11344.700| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.80 r_work: 0.2869 rms_B_bonded: 2.62 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: 0.8147 moved from start: 0.2008 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= 0.188 Angle : 0.488 5.964 12156 Z= 0.255 Chirality : 0.039 0.134 1436 Planarity : 0.004 0.036 1484 Dihedral : 11.185 88.744 1436 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.62 % Allowed : 13.78 % Favored : 84.59 % 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: 1.06 (0.26), residues: 1124 helix: 1.86 (0.19), residues: 792 sheet: 0.58 (0.64), residues: 40 loop : -2.70 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.004 0.001 HIS B 619 PHE 0.016 0.001 PHE B 61 TYR 0.013 0.001 TYR B 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 104 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.989 Fit side-chains REVERT: A 84 TRP cc_start: 0.7074 (t60) cc_final: 0.6719 (t60) REVERT: A 531 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8545 (mp) REVERT: B 84 TRP cc_start: 0.7003 (t60) cc_final: 0.6726 (t60) REVERT: B 117 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7299 (m) REVERT: B 531 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8542 (mp) outliers start: 12 outliers final: 9 residues processed: 101 average time/residue: 0.1736 time to fit residues: 26.0862 Evaluate side-chains 101 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 0.0670 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 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: 0.9920 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.125100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096804 restraints weight = 11255.538| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.79 r_work: 0.2895 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.003 0.044 8904 Z= 0.209 Angle : 0.499 5.610 12156 Z= 0.261 Chirality : 0.039 0.137 1436 Planarity : 0.004 0.036 1484 Dihedral : 11.021 85.255 1436 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.62 % Allowed : 14.19 % 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 (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: 1.03 (0.26), residues: 1124 helix: 1.83 (0.19), residues: 798 sheet: 0.70 (0.69), residues: 40 loop : -2.80 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.005 0.001 HIS B 619 PHE 0.017 0.001 PHE B 61 TYR 0.014 0.001 TYR A 589 ARG 0.001 0.000 ARG B 237 *********************** 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 100 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.932 Fit side-chains REVERT: A 84 TRP cc_start: 0.7198 (t60) cc_final: 0.6820 (t60) REVERT: A 531 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8643 (mp) REVERT: B 84 TRP cc_start: 0.7168 (t60) cc_final: 0.6821 (t60) REVERT: B 117 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7455 (m) REVERT: B 531 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8642 (mp) outliers start: 12 outliers final: 9 residues processed: 97 average time/residue: 0.1696 time to fit residues: 24.5843 Evaluate side-chains 99 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 35 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 67 optimal weight: 0.0050 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5206 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.127459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.099161 restraints weight = 11114.294| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.79 r_work: 0.2910 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2115 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= 0.145 Angle : 0.474 5.910 12156 Z= 0.247 Chirality : 0.038 0.128 1436 Planarity : 0.004 0.036 1484 Dihedral : 10.592 79.296 1436 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.35 % Allowed : 14.73 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1124 helix: 1.96 (0.19), residues: 804 sheet: 0.72 (0.70), residues: 40 loop : -2.86 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.005 0.001 HIS B 619 PHE 0.014 0.001 PHE B 61 TYR 0.011 0.001 TYR B 589 ARG 0.001 0.000 ARG B 237 ********************** 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 102 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.999 Fit side-chains REVERT: A 84 TRP cc_start: 0.7126 (t60) cc_final: 0.6780 (t60) REVERT: A 551 ILE cc_start: 0.8815 (tt) cc_final: 0.8531 (tt) REVERT: B 84 TRP cc_start: 0.7100 (t60) cc_final: 0.6762 (t60) REVERT: B 117 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7286 (m) REVERT: B 531 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8529 (mp) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.1706 time to fit residues: 25.3190 Evaluate side-chains 98 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.9980 chunk 67 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 94 optimal weight: 0.0970 chunk 108 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.126882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.098512 restraints weight = 11104.325| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.79 r_work: 0.2920 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8904 Z= 0.155 Angle : 0.475 5.576 12156 Z= 0.248 Chirality : 0.038 0.132 1436 Planarity : 0.004 0.036 1484 Dihedral : 10.294 75.431 1436 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.22 % Allowed : 15.27 % Favored : 83.51 % 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: 1.27 (0.26), residues: 1124 helix: 2.02 (0.19), residues: 804 sheet: 0.79 (0.70), residues: 40 loop : -2.84 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 227 HIS 0.004 0.001 HIS B 619 PHE 0.014 0.001 PHE B 61 TYR 0.012 0.001 TYR B 589 ARG 0.001 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4268.97 seconds wall clock time: 76 minutes 6.33 seconds (4566.33 seconds total)