Starting phenix.real_space_refine on Sat Jun 7 15:54:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3c_35149/06_2025/8i3c_35149.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3c_35149/06_2025/8i3c_35149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3c_35149/06_2025/8i3c_35149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3c_35149/06_2025/8i3c_35149.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3c_35149/06_2025/8i3c_35149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3c_35149/06_2025/8i3c_35149.cif" } resolution = 2.85 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= 0.003 sd= 0.090 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5660 2.51 5 N 1440 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8664 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4297 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 533} Chain breaks: 4 Chain: "B" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4297 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 533} Chain breaks: 4 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.58, per 1000 atoms: 0.64 Number of scatterers: 8664 At special positions: 0 Unit cell: (80.51, 100.43, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1506 8.00 N 1440 7.00 C 5660 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: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 59.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 137 through 140 removed outlier: 3.621A pdb=" N LYS A 140 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.891A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.534A pdb=" N CYS A 194 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 195 " --> pdb=" O THR A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 195' Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.522A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.925A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.575A pdb=" N PHE A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.601A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.535A pdb=" N ALA A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.057A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.951A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.615A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.517A pdb=" N LEU A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.534A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.605A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 486 " --> pdb=" O MET A 482 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.874A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.896A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.829A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.058A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.532A pdb=" N LEU A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.619A pdb=" N GLU A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 628 " --> pdb=" O PHE A 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 623 through 628' Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 643 through 660 removed outlier: 3.675A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 137 through 140 removed outlier: 3.621A pdb=" N LYS B 140 " --> pdb=" O GLN B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 183 through 189 removed outlier: 3.892A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.534A pdb=" N CYS B 194 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 195' Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.524A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.925A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.575A pdb=" N PHE B 275 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.600A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.537A pdb=" N ALA B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 4.057A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 357' Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.952A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 404' Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.615A pdb=" N PHE B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 3.517A pdb=" N LEU B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.534A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 477 through 492 removed outlier: 3.605A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 486 " --> pdb=" O MET B 482 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.874A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.896A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.828A pdb=" N LYS B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.058A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 605 removed outlier: 3.531A pdb=" N LEU B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.619A pdb=" N GLU B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 628 " --> pdb=" O PHE B 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 623 through 628' Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 643 through 660 removed outlier: 3.675A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 653 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.260A pdb=" N ILE A 83 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ARG A 48 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 85 " --> pdb=" O CYS A 46 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS A 46 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A 42 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 128 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.360A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 277 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 91 removed outlier: 6.260A pdb=" N ILE B 83 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG B 48 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 85 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS B 46 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE B 42 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 128 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP B 44 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS B 126 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.359A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 277 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 290 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1089 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: 2.22 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1314 1.29 - 1.42: 2294 1.42 - 1.55: 5136 1.55 - 1.68: 12 1.68 - 1.81: 92 Bond restraints: 8848 Sorted by residual: bond pdb=" C PHE A 441 " pdb=" O PHE A 441 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.28e-02 6.10e+03 4.00e+01 bond pdb=" C PHE B 441 " pdb=" O PHE B 441 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.34e-02 5.57e+03 3.64e+01 bond pdb=" C ILE A 445 " pdb=" O ILE A 445 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.23e-02 6.61e+03 2.48e+01 bond pdb=" C ILE B 445 " pdb=" O ILE B 445 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.23e-02 6.61e+03 2.37e+01 bond pdb=" C GLY B 438 " pdb=" O GLY B 438 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.35e-02 5.49e+03 2.18e+01 ... (remaining 8843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 11157 1.77 - 3.55: 660 3.55 - 5.32: 130 5.32 - 7.09: 41 7.09 - 8.87: 12 Bond angle restraints: 12000 Sorted by residual: angle pdb=" N VAL B 641 " pdb=" CA VAL B 641 " pdb=" C VAL B 641 " ideal model delta sigma weight residual 112.96 106.90 6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" N VAL A 641 " pdb=" CA VAL A 641 " pdb=" C VAL A 641 " ideal model delta sigma weight residual 112.96 106.93 6.03 1.00e+00 1.00e+00 3.64e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 112.96 107.88 5.08 1.00e+00 1.00e+00 2.58e+01 angle pdb=" N VAL B 414 " pdb=" CA VAL B 414 " pdb=" C VAL B 414 " ideal model delta sigma weight residual 112.96 107.90 5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" N ASP B 435 " pdb=" CA ASP B 435 " pdb=" C ASP B 435 " ideal model delta sigma weight residual 113.50 107.59 5.91 1.23e+00 6.61e-01 2.31e+01 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 4981 23.53 - 47.06: 260 47.06 - 70.59: 45 70.59 - 94.13: 14 94.13 - 117.66: 4 Dihedral angle restraints: 5304 sinusoidal: 2146 harmonic: 3158 Sorted by residual: dihedral pdb=" CA ILE A 660 " pdb=" C ILE A 660 " pdb=" N LYS A 661 " pdb=" CA LYS A 661 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LYS B 661 " pdb=" CA LYS B 661 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LYS B 285 " pdb=" C LYS B 285 " pdb=" N CYS B 286 " pdb=" CA CYS B 286 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1037 0.057 - 0.113: 325 0.113 - 0.170: 54 0.170 - 0.226: 9 0.226 - 0.283: 7 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CB VAL B 566 " pdb=" CA VAL B 566 " pdb=" CG1 VAL B 566 " pdb=" CG2 VAL B 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB VAL B 559 " pdb=" CA VAL B 559 " pdb=" CG1 VAL B 559 " pdb=" CG2 VAL B 559 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1429 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 661 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS B 661 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 661 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS B 662 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 661 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS A 661 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS A 661 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS A 662 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 350 " -0.049 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO B 351 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 351 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 351 " -0.042 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2793 2.83 - 3.35: 7222 3.35 - 3.87: 13519 3.87 - 4.38: 16632 4.38 - 4.90: 29168 Nonbonded interactions: 69334 Sorted by model distance: nonbonded pdb=" O SER A 472 " pdb=" OG SER A 472 " model vdw 2.313 3.040 nonbonded pdb=" NH2 ARG A 470 " pdb=" O LYS A 661 " model vdw 2.314 3.120 nonbonded pdb=" O SER B 472 " pdb=" OG SER B 472 " model vdw 2.314 3.040 nonbonded pdb=" NH2 ARG B 470 " pdb=" O LYS B 661 " model vdw 2.314 3.120 nonbonded pdb=" OE1 GLU A 462 " pdb=" OH TYR A 480 " model vdw 2.320 3.040 ... (remaining 69329 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.530 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.009 0.081 8848 Z= 0.443 Angle : 1.023 8.868 12000 Z= 0.581 Chirality : 0.058 0.283 1432 Planarity : 0.008 0.075 1460 Dihedral : 15.628 117.658 3276 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.81 % Allowed : 6.50 % Favored : 91.68 % 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: -6.17 (0.16), residues: 1084 helix: -4.71 (0.07), residues: 600 sheet: -1.01 (0.57), residues: 80 loop : -3.41 (0.24), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 425 HIS 0.006 0.001 HIS A 427 PHE 0.020 0.002 PHE A 499 TYR 0.035 0.003 TYR A 475 ARG 0.003 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.32219 ( 373) hydrogen bonds : angle 11.19130 ( 1089) covalent geometry : bond 0.00939 ( 8848) covalent geometry : angle 1.02255 (12000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.959 Fit side-chains REVERT: A 491 MET cc_start: 0.8585 (mmp) cc_final: 0.8367 (mmt) REVERT: B 491 MET cc_start: 0.8600 (mmp) cc_final: 0.8392 (mmp) outliers start: 17 outliers final: 4 residues processed: 167 average time/residue: 1.4259 time to fit residues: 251.8010 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 531 GLN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119515 restraints weight = 9246.727| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.82 r_work: 0.3119 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8848 Z= 0.129 Angle : 0.606 6.636 12000 Z= 0.310 Chirality : 0.041 0.161 1432 Planarity : 0.006 0.054 1460 Dihedral : 9.755 99.797 1346 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.84 % Allowed : 12.47 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.20), residues: 1084 helix: -2.41 (0.16), residues: 602 sheet: -0.99 (0.52), residues: 80 loop : -2.89 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.003 0.001 HIS B 434 PHE 0.008 0.001 PHE A 499 TYR 0.027 0.001 TYR A 475 ARG 0.007 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.04022 ( 373) hydrogen bonds : angle 4.69256 ( 1089) covalent geometry : bond 0.00297 ( 8848) covalent geometry : angle 0.60572 (12000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7073 (ptpp) cc_final: 0.6714 (mttt) REVERT: A 174 THR cc_start: 0.7807 (m) cc_final: 0.7466 (t) REVERT: A 232 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: A 300 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: B 174 THR cc_start: 0.7794 (m) cc_final: 0.7563 (t) REVERT: B 183 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7813 (mm-30) REVERT: B 450 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8176 (tp) REVERT: B 626 GLU cc_start: 0.6872 (pt0) cc_final: 0.6161 (pm20) outliers start: 36 outliers final: 8 residues processed: 154 average time/residue: 1.2223 time to fit residues: 201.7248 Evaluate side-chains 134 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 0.0270 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 266 GLN A 461 GLN B 154 HIS B 461 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116350 restraints weight = 9313.454| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.79 r_work: 0.3106 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8848 Z= 0.153 Angle : 0.606 8.016 12000 Z= 0.301 Chirality : 0.041 0.145 1432 Planarity : 0.005 0.044 1460 Dihedral : 7.428 63.663 1339 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.62 % Allowed : 14.07 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.23), residues: 1084 helix: -1.15 (0.20), residues: 638 sheet: -0.92 (0.51), residues: 80 loop : -2.78 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS A 434 PHE 0.009 0.001 PHE B 203 TYR 0.027 0.002 TYR A 475 ARG 0.009 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 373) hydrogen bonds : angle 4.11024 ( 1089) covalent geometry : bond 0.00369 ( 8848) covalent geometry : angle 0.60560 (12000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.921 Fit side-chains REVERT: A 141 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.5738 (mtp85) REVERT: A 174 THR cc_start: 0.7811 (m) cc_final: 0.7461 (t) REVERT: A 183 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7836 (mm-30) REVERT: A 232 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: A 408 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8349 (mp) REVERT: A 626 GLU cc_start: 0.6784 (pt0) cc_final: 0.6103 (pm20) REVERT: B 174 THR cc_start: 0.7605 (m) cc_final: 0.7317 (t) REVERT: B 232 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: B 266 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: B 408 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8347 (mp) REVERT: B 626 GLU cc_start: 0.6914 (pt0) cc_final: 0.6230 (pm20) outliers start: 34 outliers final: 11 residues processed: 140 average time/residue: 1.1927 time to fit residues: 178.1651 Evaluate side-chains 137 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 461 GLN A 662 HIS B 461 GLN B 662 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.163168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117354 restraints weight = 9275.155| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.82 r_work: 0.3099 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8848 Z= 0.172 Angle : 0.591 5.452 12000 Z= 0.298 Chirality : 0.042 0.146 1432 Planarity : 0.005 0.038 1460 Dihedral : 6.333 60.296 1338 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.48 % Allowed : 14.18 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.24), residues: 1084 helix: -0.66 (0.21), residues: 638 sheet: -0.84 (0.52), residues: 80 loop : -2.56 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 447 HIS 0.003 0.001 HIS B 484 PHE 0.010 0.001 PHE A 499 TYR 0.027 0.002 TYR B 475 ARG 0.008 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 373) hydrogen bonds : angle 3.99107 ( 1089) covalent geometry : bond 0.00419 ( 8848) covalent geometry : angle 0.59083 (12000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 0.997 Fit side-chains REVERT: A 141 ARG cc_start: 0.6556 (OUTLIER) cc_final: 0.5715 (mtp85) REVERT: A 183 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7845 (mm-30) REVERT: A 232 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: A 302 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7466 (m) REVERT: A 626 GLU cc_start: 0.6807 (pt0) cc_final: 0.6143 (pm20) REVERT: B 141 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.5449 (mtp85) REVERT: B 174 THR cc_start: 0.7619 (m) cc_final: 0.7293 (t) REVERT: B 183 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7860 (mm-30) REVERT: B 232 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: B 266 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8107 (mt0) REVERT: B 286 CYS cc_start: 0.7233 (t) cc_final: 0.6942 (t) REVERT: B 626 GLU cc_start: 0.6890 (pt0) cc_final: 0.6201 (pm20) outliers start: 42 outliers final: 15 residues processed: 151 average time/residue: 1.1632 time to fit residues: 187.9396 Evaluate side-chains 147 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.164150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.119007 restraints weight = 9243.397| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.76 r_work: 0.3164 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8848 Z= 0.152 Angle : 0.572 5.629 12000 Z= 0.288 Chirality : 0.042 0.140 1432 Planarity : 0.004 0.039 1460 Dihedral : 5.996 57.970 1338 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.05 % Allowed : 15.25 % Favored : 80.70 % 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: -1.66 (0.25), residues: 1084 helix: -0.32 (0.21), residues: 640 sheet: -1.14 (0.48), residues: 90 loop : -2.41 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.002 0.001 HIS B 484 PHE 0.011 0.001 PHE B 499 TYR 0.026 0.002 TYR B 475 ARG 0.010 0.000 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 373) hydrogen bonds : angle 3.86069 ( 1089) covalent geometry : bond 0.00371 ( 8848) covalent geometry : angle 0.57163 (12000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 1.011 Fit side-chains REVERT: A 141 ARG cc_start: 0.6621 (OUTLIER) cc_final: 0.5812 (mtp85) REVERT: A 183 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7855 (mm-30) REVERT: A 232 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8220 (mt-10) REVERT: A 286 CYS cc_start: 0.7200 (t) cc_final: 0.6987 (t) REVERT: A 302 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7484 (m) REVERT: B 141 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.5537 (mtp85) REVERT: B 174 THR cc_start: 0.7641 (m) cc_final: 0.7339 (t) REVERT: B 180 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6855 (mpp-170) REVERT: B 183 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: B 232 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: B 266 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: B 286 CYS cc_start: 0.7254 (t) cc_final: 0.7034 (t) REVERT: B 626 GLU cc_start: 0.6746 (pt0) cc_final: 0.6167 (pm20) outliers start: 38 outliers final: 16 residues processed: 152 average time/residue: 1.0596 time to fit residues: 173.2559 Evaluate side-chains 147 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 90 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118517 restraints weight = 9245.343| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.73 r_work: 0.3185 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8848 Z= 0.137 Angle : 0.556 5.678 12000 Z= 0.279 Chirality : 0.041 0.136 1432 Planarity : 0.004 0.044 1460 Dihedral : 5.798 55.080 1338 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.16 % Allowed : 15.88 % Favored : 79.96 % 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: -1.13 (0.25), residues: 1084 helix: 0.22 (0.22), residues: 608 sheet: -1.02 (0.48), residues: 90 loop : -2.23 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.002 0.001 HIS B 484 PHE 0.010 0.001 PHE B 499 TYR 0.025 0.002 TYR A 475 ARG 0.010 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03430 ( 373) hydrogen bonds : angle 3.77054 ( 1089) covalent geometry : bond 0.00333 ( 8848) covalent geometry : angle 0.55649 (12000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.975 Fit side-chains REVERT: A 85 SER cc_start: 0.7419 (p) cc_final: 0.7118 (t) REVERT: A 141 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.5795 (mtp85) REVERT: A 183 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7891 (mm-30) REVERT: A 232 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8222 (mt-10) REVERT: A 287 LEU cc_start: 0.6822 (mp) cc_final: 0.6605 (mt) REVERT: A 302 VAL cc_start: 0.7712 (OUTLIER) cc_final: 0.7494 (m) REVERT: B 141 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.5475 (mtp85) REVERT: B 174 THR cc_start: 0.7643 (m) cc_final: 0.7324 (t) REVERT: B 183 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7883 (mm-30) REVERT: B 232 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: B 266 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: B 286 CYS cc_start: 0.7284 (t) cc_final: 0.7057 (t) REVERT: B 626 GLU cc_start: 0.6745 (pt0) cc_final: 0.6212 (pm20) outliers start: 39 outliers final: 19 residues processed: 154 average time/residue: 1.0489 time to fit residues: 173.7171 Evaluate side-chains 148 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118130 restraints weight = 9320.442| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.82 r_work: 0.3124 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8848 Z= 0.153 Angle : 0.569 5.764 12000 Z= 0.285 Chirality : 0.042 0.137 1432 Planarity : 0.005 0.049 1460 Dihedral : 5.725 55.427 1338 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.52 % Allowed : 17.38 % Favored : 79.10 % 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: -1.14 (0.25), residues: 1084 helix: 0.15 (0.21), residues: 630 sheet: -0.94 (0.48), residues: 90 loop : -2.25 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS A 484 PHE 0.011 0.001 PHE B 499 TYR 0.025 0.002 TYR B 475 ARG 0.011 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 373) hydrogen bonds : angle 3.79950 ( 1089) covalent geometry : bond 0.00376 ( 8848) covalent geometry : angle 0.56923 (12000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 85 SER cc_start: 0.7274 (p) cc_final: 0.7027 (t) REVERT: A 136 LYS cc_start: 0.7817 (mptt) cc_final: 0.7537 (tppt) REVERT: A 141 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.5683 (mtp85) REVERT: A 183 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7808 (mm-30) REVERT: A 193 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8490 (pttm) REVERT: A 226 SER cc_start: 0.8377 (m) cc_final: 0.8103 (p) REVERT: A 232 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: A 302 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7486 (m) REVERT: B 136 LYS cc_start: 0.7829 (mptt) cc_final: 0.7544 (tppt) REVERT: B 141 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.5387 (mtp85) REVERT: B 174 THR cc_start: 0.7597 (m) cc_final: 0.7254 (t) REVERT: B 180 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6772 (mpp-170) REVERT: B 183 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: B 193 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8512 (pttm) REVERT: B 226 SER cc_start: 0.8344 (m) cc_final: 0.8055 (p) REVERT: B 232 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: B 266 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: B 286 CYS cc_start: 0.7387 (t) cc_final: 0.7128 (t) REVERT: B 626 GLU cc_start: 0.6613 (pt0) cc_final: 0.6139 (pm20) outliers start: 33 outliers final: 21 residues processed: 148 average time/residue: 1.1083 time to fit residues: 175.6043 Evaluate side-chains 157 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.165824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120648 restraints weight = 9368.052| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.79 r_work: 0.3130 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8848 Z= 0.117 Angle : 0.535 5.426 12000 Z= 0.268 Chirality : 0.040 0.131 1432 Planarity : 0.004 0.041 1460 Dihedral : 5.503 52.130 1338 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.09 % Allowed : 17.80 % Favored : 79.10 % 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: 1084 helix: 0.43 (0.22), residues: 624 sheet: -0.76 (0.47), residues: 90 loop : -2.19 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS B 427 PHE 0.010 0.001 PHE B 499 TYR 0.023 0.001 TYR B 475 ARG 0.010 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03145 ( 373) hydrogen bonds : angle 3.66790 ( 1089) covalent geometry : bond 0.00282 ( 8848) covalent geometry : angle 0.53524 (12000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 85 SER cc_start: 0.7318 (p) cc_final: 0.7035 (t) REVERT: A 193 LYS cc_start: 0.9100 (mtmm) cc_final: 0.8479 (pttm) REVERT: A 226 SER cc_start: 0.8360 (m) cc_final: 0.8045 (p) REVERT: A 283 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6670 (mt-10) REVERT: A 287 LEU cc_start: 0.6914 (mp) cc_final: 0.6713 (mt) REVERT: A 302 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7445 (m) REVERT: B 141 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.5450 (mtp85) REVERT: B 174 THR cc_start: 0.7580 (m) cc_final: 0.7269 (t) REVERT: B 180 ARG cc_start: 0.7187 (mtm110) cc_final: 0.6773 (mpp-170) REVERT: B 183 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: B 193 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8494 (pttm) REVERT: B 226 SER cc_start: 0.8374 (m) cc_final: 0.8097 (p) REVERT: B 232 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: B 266 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: B 286 CYS cc_start: 0.7368 (t) cc_final: 0.7159 (t) REVERT: B 626 GLU cc_start: 0.6428 (pt0) cc_final: 0.6008 (pm20) outliers start: 29 outliers final: 13 residues processed: 145 average time/residue: 1.0685 time to fit residues: 166.6753 Evaluate side-chains 143 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.163050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111022 restraints weight = 9294.884| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.82 r_work: 0.3102 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8848 Z= 0.184 Angle : 0.594 6.159 12000 Z= 0.297 Chirality : 0.043 0.140 1432 Planarity : 0.005 0.039 1460 Dihedral : 5.752 55.749 1338 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.99 % Allowed : 18.34 % Favored : 78.68 % 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: 1084 helix: 0.22 (0.21), residues: 634 sheet: -0.28 (0.52), residues: 80 loop : -2.04 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 447 HIS 0.002 0.001 HIS B 484 PHE 0.011 0.001 PHE B 499 TYR 0.027 0.002 TYR B 475 ARG 0.008 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 373) hydrogen bonds : angle 3.85411 ( 1089) covalent geometry : bond 0.00453 ( 8848) covalent geometry : angle 0.59445 (12000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.903 Fit side-chains REVERT: A 85 SER cc_start: 0.7317 (p) cc_final: 0.7047 (t) REVERT: A 180 ARG cc_start: 0.7221 (mtm110) cc_final: 0.6789 (mpp-170) REVERT: A 183 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7872 (mm-30) REVERT: A 193 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8496 (pttm) REVERT: A 226 SER cc_start: 0.8411 (m) cc_final: 0.8076 (p) REVERT: A 283 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6830 (mt-10) REVERT: A 302 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7491 (m) REVERT: B 141 ARG cc_start: 0.6477 (OUTLIER) cc_final: 0.5541 (mtp85) REVERT: B 174 THR cc_start: 0.7567 (m) cc_final: 0.7207 (t) REVERT: B 180 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6755 (mpp-170) REVERT: B 183 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7851 (mm-30) REVERT: B 193 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8492 (pttm) REVERT: B 226 SER cc_start: 0.8427 (m) cc_final: 0.8163 (p) REVERT: B 232 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: B 266 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: B 283 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6691 (mt-10) REVERT: B 296 MET cc_start: 0.7996 (mmm) cc_final: 0.7784 (mmm) REVERT: B 626 GLU cc_start: 0.6553 (pt0) cc_final: 0.6083 (pm20) outliers start: 28 outliers final: 15 residues processed: 144 average time/residue: 1.0866 time to fit residues: 167.5534 Evaluate side-chains 145 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.117129 restraints weight = 9306.366| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.76 r_work: 0.3167 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8848 Z= 0.158 Angle : 0.574 5.788 12000 Z= 0.287 Chirality : 0.042 0.135 1432 Planarity : 0.004 0.041 1460 Dihedral : 5.683 53.228 1338 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.56 % Allowed : 18.76 % Favored : 78.68 % 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: -0.64 (0.26), residues: 1084 helix: 0.53 (0.22), residues: 608 sheet: -0.48 (0.48), residues: 90 loop : -1.94 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.002 0.001 HIS A 484 PHE 0.011 0.001 PHE B 499 TYR 0.025 0.002 TYR B 475 ARG 0.009 0.000 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03645 ( 373) hydrogen bonds : angle 3.79098 ( 1089) covalent geometry : bond 0.00387 ( 8848) covalent geometry : angle 0.57362 (12000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.904 Fit side-chains REVERT: A 85 SER cc_start: 0.7392 (p) cc_final: 0.7063 (t) REVERT: A 180 ARG cc_start: 0.7230 (mtm110) cc_final: 0.6856 (mpp-170) REVERT: A 183 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7888 (mm-30) REVERT: A 193 LYS cc_start: 0.9110 (mtmm) cc_final: 0.8498 (pttm) REVERT: A 226 SER cc_start: 0.8451 (m) cc_final: 0.8150 (p) REVERT: A 283 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6961 (mt-10) REVERT: A 302 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7512 (m) REVERT: B 141 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.5625 (mtp85) REVERT: B 174 THR cc_start: 0.7639 (m) cc_final: 0.7315 (t) REVERT: B 180 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6821 (mpp-170) REVERT: B 183 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: B 193 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8508 (pttm) REVERT: B 226 SER cc_start: 0.8460 (m) cc_final: 0.8229 (p) REVERT: B 232 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: B 266 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8081 (mt0) REVERT: B 283 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6874 (mt-10) REVERT: B 296 MET cc_start: 0.8049 (mmm) cc_final: 0.7845 (mmm) REVERT: B 626 GLU cc_start: 0.6626 (pt0) cc_final: 0.6200 (pm20) outliers start: 24 outliers final: 16 residues processed: 139 average time/residue: 1.0938 time to fit residues: 163.5126 Evaluate side-chains 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.162712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.114948 restraints weight = 9340.891| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.72 r_work: 0.3101 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8848 Z= 0.184 Angle : 0.604 7.294 12000 Z= 0.299 Chirality : 0.043 0.139 1432 Planarity : 0.004 0.038 1460 Dihedral : 5.735 55.875 1338 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.24 % Allowed : 19.83 % Favored : 77.93 % 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: 1084 helix: 0.23 (0.21), residues: 634 sheet: -0.42 (0.48), residues: 90 loop : -2.02 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 447 HIS 0.002 0.001 HIS B 484 PHE 0.012 0.001 PHE B 499 TYR 0.026 0.002 TYR B 475 ARG 0.008 0.001 ARG A 180 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 373) hydrogen bonds : angle 3.87167 ( 1089) covalent geometry : bond 0.00453 ( 8848) covalent geometry : angle 0.60380 (12000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6827.56 seconds wall clock time: 117 minutes 18.94 seconds (7038.94 seconds total)