Starting phenix.real_space_refine on Mon Apr 6 04:33:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4a_62051/04_2026/9k4a_62051.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4a_62051/04_2026/9k4a_62051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k4a_62051/04_2026/9k4a_62051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4a_62051/04_2026/9k4a_62051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k4a_62051/04_2026/9k4a_62051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4a_62051/04_2026/9k4a_62051.map" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.064 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 75 5.16 5 C 9660 2.51 5 N 2574 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15447 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5149 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 656} Chain: "B" Number of atoms: 5149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5149 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 656} Chain: "C" Number of atoms: 5149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5149 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 656} Time building chain proxies: 3.95, per 1000 atoms: 0.26 Number of scatterers: 15447 At special positions: 0 Unit cell: (95.23, 94.16, 173.34, 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 75 16.00 O 3138 8.00 N 2574 7.00 C 9660 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: 1.43 Conformation dependent library (CDL) restraints added in 780.4 milliseconds 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3684 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 27 sheets defined 7.3% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 245 through 257 removed outlier: 3.875A pdb=" N SER A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 333 through 343 removed outlier: 4.345A pdb=" N THR A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 762 through 764 No H-bonds generated for 'chain 'A' and resid 762 through 764' Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 233 through 237 Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.875A pdb=" N SER B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 removed outlier: 4.532A pdb=" N ASN B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 333 through 343 removed outlier: 4.165A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 764 No H-bonds generated for 'chain 'B' and resid 762 through 764' Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 233 through 237 Processing helix chain 'C' and resid 245 through 257 removed outlier: 3.905A pdb=" N SER C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 343 removed outlier: 4.322A pdb=" N THR C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 729 through 733 Processing helix chain 'C' and resid 762 through 764 No H-bonds generated for 'chain 'C' and resid 762 through 764' Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 280 removed outlier: 4.741A pdb=" N TYR A 293 " --> pdb=" O ARG A 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 327 removed outlier: 6.019A pdb=" N ALA A 326 " --> pdb=" O ARG A 349 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS A 482 " --> pdb=" O CYS A 509 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN A 511 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 535 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS A 541 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP A 510 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN A 543 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY A 558 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 582 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 560 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 584 " --> pdb=" O GLU A 560 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 562 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N HIS A 580 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP A 612 " --> pdb=" O HIS A 580 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 582 " --> pdb=" O ASP A 612 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER A 609 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN A 636 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE A 611 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY A 656 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP A 655 " --> pdb=" O GLY A 680 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER A 682 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE A 657 " --> pdb=" O SER A 682 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY A 701 " --> pdb=" O ASN A 679 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR A 700 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ASP A 723 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR A 702 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR A 754 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 722 " --> pdb=" O TYR A 754 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ARG A 756 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS A 724 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 362 removed outlier: 5.973A pdb=" N LEU A 360 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER A 389 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 362 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 535 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS A 541 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP A 510 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN A 543 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU A 567 " --> pdb=" O ARG A 542 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLU A 566 " --> pdb=" O GLY A 595 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LEU A 597 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL A 568 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ASN A 599 " --> pdb=" O VAL A 568 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 570 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASN A 594 " --> pdb=" O ASN A 619 " (cutoff:3.500A) removed outlier: 9.136A pdb=" N THR A 621 " --> pdb=" O ASN A 594 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 596 " --> pdb=" O THR A 621 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N SER A 623 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE A 598 " --> pdb=" O SER A 623 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N LYS A 643 " --> pdb=" O ARG A 618 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 620 " --> pdb=" O LYS A 643 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE A 645 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N PHE A 622 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 642 " --> pdb=" O ARG A 667 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE A 669 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR A 644 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLY A 688 " --> pdb=" O ARG A 708 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE A 710 " --> pdb=" O GLY A 688 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 690 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A 707 " --> pdb=" O TYR A 737 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP A 739 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 709 " --> pdb=" O ASP A 739 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 736 " --> pdb=" O SER A 767 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS A 769 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE A 738 " --> pdb=" O LYS A 769 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 356 Processing sheet with id=AA5, first strand: chain 'A' and resid 392 through 398 removed outlier: 6.525A pdb=" N ILE A 396 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TYR A 424 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 443 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 451 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 491 removed outlier: 6.352A pdb=" N LEU A 519 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 551 " --> pdb=" O ASP A 576 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N PHE A 575 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER A 603 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 649 " --> pdb=" O THR A 674 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 810 through 814 removed outlier: 6.535A pdb=" N THR A 881 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 823 removed outlier: 6.655A pdb=" N SER A 868 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ILE A 863 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR A 870 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 829 through 830 Processing sheet with id=AB1, first strand: chain 'B' and resid 277 through 280 removed outlier: 4.755A pdb=" N TYR B 293 " --> pdb=" O ARG B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 326 through 327 removed outlier: 6.000A pdb=" N ALA B 326 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS B 482 " --> pdb=" O CYS B 509 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 511 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN B 543 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU B 567 " --> pdb=" O ARG B 542 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU B 566 " --> pdb=" O GLY B 595 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LEU B 597 " --> pdb=" O GLU B 566 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASN B 599 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 570 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASN B 594 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N THR B 621 " --> pdb=" O ASN B 594 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE B 596 " --> pdb=" O THR B 621 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N SER B 623 " --> pdb=" O ILE B 596 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE B 598 " --> pdb=" O SER B 623 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N LYS B 643 " --> pdb=" O ARG B 618 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 620 " --> pdb=" O LYS B 643 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE B 645 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE B 622 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 642 " --> pdb=" O ARG B 667 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N ILE B 669 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR B 644 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N THR B 666 " --> pdb=" O ASN B 689 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLU B 691 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 668 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY B 688 " --> pdb=" O ARG B 708 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE B 710 " --> pdb=" O GLY B 688 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE B 690 " --> pdb=" O ILE B 710 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 354 through 356 Processing sheet with id=AB4, first strand: chain 'B' and resid 360 through 362 removed outlier: 5.896A pdb=" N LEU B 360 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER B 389 " --> pdb=" O LEU B 360 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 362 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 386 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL B 507 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N CYS B 388 " --> pdb=" O VAL B 507 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N MET B 504 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASN B 539 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET B 506 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL B 582 " --> pdb=" O GLY B 558 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU B 560 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 584 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 562 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N HIS B 580 " --> pdb=" O GLY B 610 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP B 612 " --> pdb=" O HIS B 580 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL B 582 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER B 609 " --> pdb=" O GLY B 634 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN B 636 " --> pdb=" O SER B 609 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 611 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY B 656 " --> pdb=" O ASP B 633 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASP B 655 " --> pdb=" O GLY B 680 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N SER B 682 " --> pdb=" O ASP B 655 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE B 657 " --> pdb=" O SER B 682 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY B 701 " --> pdb=" O ASN B 679 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS B 721 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR B 754 " --> pdb=" O ALA B 720 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 722 " --> pdb=" O TYR B 754 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ARG B 756 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N CYS B 724 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 392 through 398 removed outlier: 6.519A pdb=" N ILE B 396 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR B 424 " --> pdb=" O MET B 478 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 443 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 451 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 490 through 491 removed outlier: 6.391A pdb=" N ALA B 551 " --> pdb=" O ASP B 576 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE B 575 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER B 603 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA B 627 " --> pdb=" O ASP B 650 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA B 649 " --> pdb=" O THR B 674 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 811 through 814 removed outlier: 6.590A pdb=" N THR B 881 " --> pdb=" O ILE B 849 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 819 through 823 removed outlier: 6.663A pdb=" N SER B 868 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE B 863 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR B 870 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 829 through 830 Processing sheet with id=AC1, first strand: chain 'C' and resid 277 through 280 removed outlier: 4.753A pdb=" N TYR C 293 " --> pdb=" O ARG C 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 326 through 327 removed outlier: 5.964A pdb=" N ALA C 326 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR C 366 " --> pdb=" O ASN C 485 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASP C 487 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU C 368 " --> pdb=" O ASP C 487 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS C 482 " --> pdb=" O CYS C 509 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ASN C 511 " --> pdb=" O LYS C 482 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR C 503 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N ILE C 538 " --> pdb=" O THR C 503 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N ASN C 505 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N SER C 540 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL C 507 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ARG C 542 " --> pdb=" O VAL C 507 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N CYS C 509 " --> pdb=" O ARG C 542 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C 544 " --> pdb=" O CYS C 509 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN C 511 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ILE C 546 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL C 513 " --> pdb=" O ILE C 546 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY C 558 " --> pdb=" O THR C 534 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 582 " --> pdb=" O GLY C 558 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU C 560 " --> pdb=" O VAL C 582 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 584 " --> pdb=" O GLU C 560 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 562 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS C 580 " --> pdb=" O GLY C 610 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP C 612 " --> pdb=" O HIS C 580 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 582 " --> pdb=" O ASP C 612 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER C 609 " --> pdb=" O GLY C 634 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN C 636 " --> pdb=" O SER C 609 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE C 611 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 656 " --> pdb=" O ASP C 633 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP C 655 " --> pdb=" O GLY C 680 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N SER C 682 " --> pdb=" O ASP C 655 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE C 657 " --> pdb=" O SER C 682 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY C 701 " --> pdb=" O ASN C 679 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR C 700 " --> pdb=" O CYS C 721 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP C 723 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR C 702 " --> pdb=" O ASP C 723 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR C 754 " --> pdb=" O ALA C 720 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C 722 " --> pdb=" O TYR C 754 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ARG C 756 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N CYS C 724 " --> pdb=" O ARG C 756 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 360 through 361 removed outlier: 5.948A pdb=" N LEU C 360 " --> pdb=" O ILE C 387 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER C 389 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N THR C 503 " --> pdb=" O LEU C 536 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N ILE C 538 " --> pdb=" O THR C 503 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N ASN C 505 " --> pdb=" O ILE C 538 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N SER C 540 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL C 507 " --> pdb=" O SER C 540 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ARG C 542 " --> pdb=" O VAL C 507 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N CYS C 509 " --> pdb=" O ARG C 542 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C 544 " --> pdb=" O CYS C 509 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ASN C 511 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N ILE C 546 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL C 513 " --> pdb=" O ILE C 546 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU C 567 " --> pdb=" O ARG C 542 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N GLU C 566 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N LEU C 597 " --> pdb=" O GLU C 566 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL C 568 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASN C 599 " --> pdb=" O VAL C 568 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 570 " --> pdb=" O ASN C 599 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN C 594 " --> pdb=" O ASN C 619 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N THR C 621 " --> pdb=" O ASN C 594 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE C 596 " --> pdb=" O THR C 621 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N SER C 623 " --> pdb=" O ILE C 596 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE C 598 " --> pdb=" O SER C 623 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N LYS C 643 " --> pdb=" O ARG C 618 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE C 620 " --> pdb=" O LYS C 643 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE C 645 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE C 622 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL C 642 " --> pdb=" O ARG C 667 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE C 669 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 644 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR C 666 " --> pdb=" O ASN C 689 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N GLU C 691 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU C 668 " --> pdb=" O GLU C 691 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLY C 688 " --> pdb=" O ARG C 708 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ILE C 710 " --> pdb=" O GLY C 688 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 690 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU C 736 " --> pdb=" O SER C 767 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LYS C 769 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 738 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 354 through 356 Processing sheet with id=AC5, first strand: chain 'C' and resid 392 through 398 removed outlier: 6.540A pdb=" N ILE C 396 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR C 424 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 443 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS C 451 " --> pdb=" O TYR C 458 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 490 through 491 removed outlier: 6.354A pdb=" N LEU C 519 " --> pdb=" O TYR C 552 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA C 551 " --> pdb=" O ASP C 576 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 575 " --> pdb=" O THR C 604 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER C 603 " --> pdb=" O TYR C 628 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA C 627 " --> pdb=" O ASP C 650 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA C 649 " --> pdb=" O THR C 674 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 810 through 814 removed outlier: 6.469A pdb=" N THR C 881 " --> pdb=" O ILE C 849 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 819 through 823 removed outlier: 6.674A pdb=" N SER C 868 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C 863 " --> pdb=" O SER C 868 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR C 870 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 829 through 830 370 hydrogen bonds defined for protein. 981 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: 3.55 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 5018 1.34 - 1.48: 4120 1.48 - 1.62: 6468 1.62 - 1.76: 1 1.76 - 1.90: 98 Bond restraints: 15705 Sorted by residual: bond pdb=" CB ARG A 428 " pdb=" CG ARG A 428 " ideal model delta sigma weight residual 1.520 1.411 0.109 3.00e-02 1.11e+03 1.33e+01 bond pdb=" CZ ARG C 447 " pdb=" NH2 ARG C 447 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.86e+00 bond pdb=" CB ARG A 349 " pdb=" CG ARG A 349 " ideal model delta sigma weight residual 1.520 1.604 -0.084 3.00e-02 1.11e+03 7.83e+00 bond pdb=" CA PHE C 500 " pdb=" CB PHE C 500 " ideal model delta sigma weight residual 1.538 1.608 -0.069 2.55e-02 1.54e+03 7.41e+00 bond pdb=" CB CYS C 671 " pdb=" SG CYS C 671 " ideal model delta sigma weight residual 1.808 1.898 -0.090 3.30e-02 9.18e+02 7.36e+00 ... (remaining 15700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 19581 2.25 - 4.50: 1516 4.50 - 6.75: 185 6.75 - 8.99: 39 8.99 - 11.24: 12 Bond angle restraints: 21333 Sorted by residual: angle pdb=" N ASN B 585 " pdb=" CA ASN B 585 " pdb=" C ASN B 585 " ideal model delta sigma weight residual 110.53 119.31 -8.78 1.32e+00 5.74e-01 4.42e+01 angle pdb=" N THR B 503 " pdb=" CA THR B 503 " pdb=" C THR B 503 " ideal model delta sigma weight residual 111.14 116.84 -5.70 1.08e+00 8.57e-01 2.78e+01 angle pdb=" C ASP B 729 " pdb=" N PRO B 730 " pdb=" CA PRO B 730 " ideal model delta sigma weight residual 119.05 124.50 -5.45 1.11e+00 8.12e-01 2.41e+01 angle pdb=" N ASP B 723 " pdb=" CA ASP B 723 " pdb=" C ASP B 723 " ideal model delta sigma weight residual 108.52 100.85 7.67 1.63e+00 3.76e-01 2.21e+01 angle pdb=" CB ILE B 512 " pdb=" CG1 ILE B 512 " pdb=" CD1 ILE B 512 " ideal model delta sigma weight residual 113.80 103.95 9.85 2.10e+00 2.27e-01 2.20e+01 ... (remaining 21328 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.46: 8399 15.46 - 30.92: 704 30.92 - 46.37: 136 46.37 - 61.83: 26 61.83 - 77.29: 17 Dihedral angle restraints: 9282 sinusoidal: 3498 harmonic: 5784 Sorted by residual: dihedral pdb=" CA ASN A 717 " pdb=" C ASN A 717 " pdb=" N SER A 718 " pdb=" CA SER A 718 " ideal model delta harmonic sigma weight residual -180.00 -156.04 -23.96 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASN B 717 " pdb=" C ASN B 717 " pdb=" N SER B 718 " pdb=" CA SER B 718 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 520 " pdb=" C TYR B 520 " pdb=" N GLY B 521 " pdb=" CA GLY B 521 " ideal model delta harmonic sigma weight residual 180.00 156.34 23.66 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 9279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1957 0.097 - 0.194: 448 0.194 - 0.291: 60 0.291 - 0.389: 12 0.389 - 0.486: 4 Chirality restraints: 2481 Sorted by residual: chirality pdb=" CB VAL C 544 " pdb=" CA VAL C 544 " pdb=" CG1 VAL C 544 " pdb=" CG2 VAL C 544 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" CB ILE C 596 " pdb=" CA ILE C 596 " pdb=" CG1 ILE C 596 " pdb=" CG2 ILE C 596 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CB VAL B 544 " pdb=" CA VAL B 544 " pdb=" CG1 VAL B 544 " pdb=" CG2 VAL B 544 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.84e+00 ... (remaining 2478 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 586 " 0.056 2.00e-02 2.50e+03 4.95e-02 6.13e+01 pdb=" CG TRP A 586 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 TRP A 586 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A 586 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 586 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 586 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 586 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 586 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 586 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 586 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 586 " 0.054 2.00e-02 2.50e+03 4.61e-02 5.32e+01 pdb=" CG TRP C 586 " -0.122 2.00e-02 2.50e+03 pdb=" CD1 TRP C 586 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP C 586 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 586 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP C 586 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 586 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 586 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 586 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 586 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 552 " -0.013 2.00e-02 2.50e+03 3.72e-02 2.76e+01 pdb=" CG TYR B 552 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TYR B 552 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR B 552 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 552 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 552 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 552 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 552 " 0.020 2.00e-02 2.50e+03 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1787 2.75 - 3.28: 15814 3.28 - 3.82: 28177 3.82 - 4.36: 37732 4.36 - 4.90: 61254 Nonbonded interactions: 144764 Sorted by model distance: nonbonded pdb=" OG SER C 522 " pdb=" N GLY C 555 " model vdw 2.208 3.120 nonbonded pdb=" ND2 ASN A 437 " pdb=" O VAL A 441 " model vdw 2.218 3.120 nonbonded pdb=" O ASN C 798 " pdb=" OG SER C 887 " model vdw 2.226 3.040 nonbonded pdb=" NH2 ARG C 848 " pdb=" O GLY C 856 " model vdw 2.240 3.120 nonbonded pdb=" OE2 GLU A 592 " pdb=" NE ARG A 618 " model vdw 2.240 3.120 ... (remaining 144759 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.140 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.250 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.011 0.109 15705 Z= 0.502 Angle : 1.311 11.243 21333 Z= 0.739 Chirality : 0.085 0.486 2481 Planarity : 0.011 0.051 2748 Dihedral : 12.651 77.288 5598 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.28 % Allowed : 2.55 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 1998 helix: -1.32 (0.47), residues: 81 sheet: 0.51 (0.21), residues: 600 loop : -0.65 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 542 TYR 0.086 0.008 TYR B 552 PHE 0.069 0.009 PHE B 681 TRP 0.129 0.006 TRP A 586 HIS 0.017 0.006 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.01078 (15705) covalent geometry : angle 1.31078 (21333) hydrogen bonds : bond 0.15774 ( 361) hydrogen bonds : angle 7.29677 ( 981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 269 time to evaluate : 0.575 Fit side-chains REVERT: A 284 THR cc_start: 0.8151 (p) cc_final: 0.7835 (p) REVERT: A 314 ASN cc_start: 0.7966 (m110) cc_final: 0.7667 (m-40) REVERT: A 358 LYS cc_start: 0.7444 (ptpt) cc_final: 0.7004 (tptp) REVERT: B 453 ASP cc_start: 0.7212 (t0) cc_final: 0.6922 (p0) REVERT: C 247 GLN cc_start: 0.7436 (tp40) cc_final: 0.6953 (mm110) REVERT: C 268 LYS cc_start: 0.7427 (ptpp) cc_final: 0.7211 (mmtp) REVERT: C 487 ASP cc_start: 0.8273 (t0) cc_final: 0.7886 (t0) REVERT: C 632 ASP cc_start: 0.7291 (t0) cc_final: 0.7077 (t0) REVERT: C 794 MET cc_start: 0.7430 (mtm) cc_final: 0.7192 (mtm) outliers start: 5 outliers final: 4 residues processed: 273 average time/residue: 0.4982 time to fit residues: 153.5031 Evaluate side-chains 151 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 147 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain C residue 552 TYR Chi-restraints excluded: chain C residue 855 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 ASN A 511 ASN A 518 GLN A 599 ASN A 614 HIS A 659 GLN A 665 ASN A 679 ASN A 699 GLN A 796 ASN A 797 ASN B 365 ASN B 371 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 ASN B 485 ASN B 511 ASN B 599 ASN B 665 ASN B 689 ASN B 854 ASN C 371 ASN C 483 ASN C 495 ASN C 511 ASN C 665 ASN C 689 ASN C 796 ASN C 797 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.170606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.149733 restraints weight = 14962.623| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.11 r_work: 0.3787 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15705 Z= 0.139 Angle : 0.564 9.834 21333 Z= 0.319 Chirality : 0.048 0.169 2481 Planarity : 0.003 0.030 2748 Dihedral : 5.665 24.362 2176 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.81 % Allowed : 8.45 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 1998 helix: -0.37 (0.56), residues: 84 sheet: 0.49 (0.20), residues: 606 loop : -0.60 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 321 TYR 0.021 0.002 TYR B 520 PHE 0.020 0.002 PHE A 500 TRP 0.031 0.002 TRP C 586 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd covalent geometry : bond 0.00283 (15705) covalent geometry : angle 0.56386 (21333) hydrogen bonds : bond 0.04023 ( 361) hydrogen bonds : angle 5.53588 ( 981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.596 Fit side-chains REVERT: A 284 THR cc_start: 0.8163 (p) cc_final: 0.7859 (p) REVERT: A 358 LYS cc_start: 0.7345 (ptpt) cc_final: 0.6835 (tptp) REVERT: A 854 ASN cc_start: 0.7373 (m110) cc_final: 0.7159 (m110) REVERT: B 358 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6855 (ptmm) REVERT: B 487 ASP cc_start: 0.7152 (OUTLIER) cc_final: 0.6581 (t70) REVERT: B 618 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8201 (mtt-85) REVERT: B 709 ILE cc_start: 0.8338 (mt) cc_final: 0.7953 (tt) REVERT: C 247 GLN cc_start: 0.7065 (tp40) cc_final: 0.6380 (mm-40) REVERT: C 277 GLU cc_start: 0.5914 (tt0) cc_final: 0.5601 (tt0) REVERT: C 487 ASP cc_start: 0.7889 (t0) cc_final: 0.7545 (t0) REVERT: C 495 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7189 (p0) REVERT: C 547 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6614 (tp30) REVERT: C 585 ASN cc_start: 0.7809 (t0) cc_final: 0.7582 (t0) REVERT: C 794 MET cc_start: 0.7433 (mtm) cc_final: 0.7152 (mtm) REVERT: C 855 ILE cc_start: 0.8028 (mt) cc_final: 0.7814 (mm) REVERT: C 865 ASN cc_start: 0.8135 (t0) cc_final: 0.7928 (t0) outliers start: 32 outliers final: 14 residues processed: 207 average time/residue: 0.4669 time to fit residues: 109.9215 Evaluate side-chains 161 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 418 LYS Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 739 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 862 ASN Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 718 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 689 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 854 ASN C 485 ASN C 495 ASN C 796 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141074 restraints weight = 15087.432| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.12 r_work: 0.3693 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15705 Z= 0.224 Angle : 0.655 11.446 21333 Z= 0.368 Chirality : 0.051 0.170 2481 Planarity : 0.004 0.036 2748 Dihedral : 6.000 27.068 2169 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 2.04 % Allowed : 11.00 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 1998 helix: -0.61 (0.51), residues: 84 sheet: 0.06 (0.18), residues: 762 loop : -0.72 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 321 TYR 0.024 0.002 TYR C 465 PHE 0.021 0.003 PHE A 491 TRP 0.027 0.002 TRP C 586 HIS 0.004 0.002 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00487 (15705) covalent geometry : angle 0.65521 (21333) hydrogen bonds : bond 0.04666 ( 361) hydrogen bonds : angle 5.75731 ( 981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.681 Fit side-chains REVERT: A 284 THR cc_start: 0.8170 (p) cc_final: 0.7821 (p) REVERT: A 286 ASN cc_start: 0.7783 (m-40) cc_final: 0.7575 (m-40) REVERT: A 358 LYS cc_start: 0.7726 (ptpt) cc_final: 0.7001 (tptp) REVERT: A 426 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6664 (tm-30) REVERT: B 249 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 487 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6576 (t70) REVERT: B 524 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7137 (mp0) REVERT: B 618 ARG cc_start: 0.8733 (mtt180) cc_final: 0.8510 (mtt-85) REVERT: C 247 GLN cc_start: 0.7276 (tp40) cc_final: 0.6510 (mm-40) REVERT: C 251 ASP cc_start: 0.7509 (m-30) cc_final: 0.7244 (m-30) REVERT: C 547 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6684 (tp30) REVERT: C 612 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6976 (p0) REVERT: C 794 MET cc_start: 0.7314 (mtm) cc_final: 0.7034 (mtm) outliers start: 36 outliers final: 18 residues processed: 179 average time/residue: 0.4968 time to fit residues: 100.9012 Evaluate side-chains 159 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 812 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 127 optimal weight: 0.1980 chunk 149 optimal weight: 5.9990 chunk 171 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 HIS C 495 ASN C 778 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.169152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.148046 restraints weight = 15071.763| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.13 r_work: 0.3777 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15705 Z= 0.100 Angle : 0.495 9.686 21333 Z= 0.281 Chirality : 0.046 0.170 2481 Planarity : 0.003 0.033 2748 Dihedral : 5.299 23.372 2169 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.87 % Allowed : 12.41 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.18), residues: 1998 helix: -0.05 (0.56), residues: 84 sheet: -0.06 (0.18), residues: 825 loop : -0.49 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 321 TYR 0.016 0.001 TYR B 520 PHE 0.013 0.001 PHE A 370 TRP 0.008 0.001 TRP A 586 HIS 0.002 0.001 HIS A 580 Details of bonding type rmsd covalent geometry : bond 0.00207 (15705) covalent geometry : angle 0.49514 (21333) hydrogen bonds : bond 0.03249 ( 361) hydrogen bonds : angle 5.22637 ( 981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 284 THR cc_start: 0.8194 (p) cc_final: 0.7848 (p) REVERT: A 358 LYS cc_start: 0.7627 (ptpt) cc_final: 0.7050 (tptp) REVERT: A 850 LEU cc_start: 0.8174 (tp) cc_final: 0.7838 (mm) REVERT: B 314 ASN cc_start: 0.8204 (m-40) cc_final: 0.7998 (m110) REVERT: B 358 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6799 (ptmm) REVERT: B 487 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6425 (t70) REVERT: B 618 ARG cc_start: 0.8697 (mtt180) cc_final: 0.8457 (mtt-85) REVERT: B 643 LYS cc_start: 0.8156 (mtpp) cc_final: 0.7949 (ttmp) REVERT: B 700 TYR cc_start: 0.8425 (m-80) cc_final: 0.8130 (m-80) REVERT: C 247 GLN cc_start: 0.7189 (tp40) cc_final: 0.6336 (mm-40) REVERT: C 794 MET cc_start: 0.7321 (mtm) cc_final: 0.7047 (mtm) outliers start: 33 outliers final: 19 residues processed: 184 average time/residue: 0.4967 time to fit residues: 103.4283 Evaluate side-chains 168 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 812 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 168 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 192 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN C 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.167020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.145544 restraints weight = 15056.504| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.12 r_work: 0.3745 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15705 Z= 0.134 Angle : 0.528 10.421 21333 Z= 0.298 Chirality : 0.046 0.164 2481 Planarity : 0.003 0.034 2748 Dihedral : 5.410 25.078 2169 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.78 % Allowed : 12.19 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.18), residues: 1998 helix: -0.06 (0.55), residues: 84 sheet: -0.09 (0.18), residues: 786 loop : -0.50 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 321 TYR 0.017 0.002 TYR C 520 PHE 0.015 0.002 PHE A 370 TRP 0.009 0.001 TRP A 586 HIS 0.002 0.001 HIS B 553 Details of bonding type rmsd covalent geometry : bond 0.00289 (15705) covalent geometry : angle 0.52842 (21333) hydrogen bonds : bond 0.03497 ( 361) hydrogen bonds : angle 5.22065 ( 981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 155 time to evaluate : 0.582 Fit side-chains REVERT: A 284 THR cc_start: 0.8175 (p) cc_final: 0.7825 (p) REVERT: A 358 LYS cc_start: 0.7685 (ptpt) cc_final: 0.7099 (tptp) REVERT: B 358 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6916 (ptmm) REVERT: B 418 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7818 (pttt) REVERT: B 618 ARG cc_start: 0.8720 (mtt180) cc_final: 0.8405 (mtt-85) REVERT: B 643 LYS cc_start: 0.8305 (mtpp) cc_final: 0.8082 (ttmp) REVERT: B 700 TYR cc_start: 0.8415 (m-80) cc_final: 0.8159 (m-80) REVERT: C 238 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6544 (mm) REVERT: C 247 GLN cc_start: 0.7228 (tp40) cc_final: 0.6502 (mm-40) REVERT: C 547 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6680 (tp30) REVERT: C 794 MET cc_start: 0.7258 (mtm) cc_final: 0.6972 (mtm) REVERT: C 796 ASN cc_start: 0.6976 (OUTLIER) cc_final: 0.6653 (m-40) outliers start: 49 outliers final: 30 residues processed: 189 average time/residue: 0.4899 time to fit residues: 105.1040 Evaluate side-chains 178 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 862 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 812 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 9 optimal weight: 0.0770 chunk 71 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 0.0470 chunk 72 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN C 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.164215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.142639 restraints weight = 14927.002| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.12 r_work: 0.3711 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15705 Z= 0.191 Angle : 0.605 11.244 21333 Z= 0.340 Chirality : 0.049 0.191 2481 Planarity : 0.004 0.040 2748 Dihedral : 5.786 28.199 2169 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 2.95 % Allowed : 12.59 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.18), residues: 1998 helix: -0.21 (0.53), residues: 84 sheet: -0.11 (0.20), residues: 657 loop : -0.63 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 320 TYR 0.016 0.002 TYR C 520 PHE 0.017 0.002 PHE A 370 TRP 0.010 0.001 TRP C 586 HIS 0.004 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00419 (15705) covalent geometry : angle 0.60458 (21333) hydrogen bonds : bond 0.04069 ( 361) hydrogen bonds : angle 5.50765 ( 981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 0.453 Fit side-chains REVERT: A 284 THR cc_start: 0.8198 (p) cc_final: 0.7822 (p) REVERT: A 358 LYS cc_start: 0.7770 (ptpt) cc_final: 0.7136 (tptp) REVERT: A 426 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: A 552 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: A 850 LEU cc_start: 0.8244 (tp) cc_final: 0.7952 (mm) REVERT: B 358 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6822 (ptmm) REVERT: B 618 ARG cc_start: 0.8729 (mtt180) cc_final: 0.8392 (mtt-85) REVERT: B 643 LYS cc_start: 0.8210 (mtpp) cc_final: 0.7965 (ttmp) REVERT: B 700 TYR cc_start: 0.8470 (m-80) cc_final: 0.8162 (m-80) REVERT: C 238 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6528 (mm) REVERT: C 247 GLN cc_start: 0.7215 (tp40) cc_final: 0.6915 (tp-100) REVERT: C 358 LYS cc_start: 0.7290 (ptpt) cc_final: 0.6615 (pttt) REVERT: C 547 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.6727 (tp30) REVERT: C 794 MET cc_start: 0.7310 (mtm) cc_final: 0.7000 (mtm) REVERT: C 796 ASN cc_start: 0.7011 (OUTLIER) cc_final: 0.6678 (m-40) outliers start: 52 outliers final: 28 residues processed: 188 average time/residue: 0.4847 time to fit residues: 103.0422 Evaluate side-chains 176 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 426 GLU Chi-restraints excluded: chain A residue 552 TYR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 812 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 114 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 112 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.0270 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN C 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.168947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.147742 restraints weight = 14874.932| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.13 r_work: 0.3777 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15705 Z= 0.101 Angle : 0.484 6.468 21333 Z= 0.275 Chirality : 0.045 0.160 2481 Planarity : 0.003 0.039 2748 Dihedral : 5.221 23.655 2169 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.04 % Allowed : 13.66 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.18), residues: 1998 helix: 0.27 (0.57), residues: 84 sheet: -0.14 (0.18), residues: 786 loop : -0.53 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 321 TYR 0.015 0.001 TYR B 520 PHE 0.013 0.001 PHE A 370 TRP 0.008 0.001 TRP B 272 HIS 0.003 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00213 (15705) covalent geometry : angle 0.48376 (21333) hydrogen bonds : bond 0.03054 ( 361) hydrogen bonds : angle 5.08913 ( 981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.503 Fit side-chains REVERT: A 284 THR cc_start: 0.8164 (p) cc_final: 0.7782 (p) REVERT: A 358 LYS cc_start: 0.7744 (ptpt) cc_final: 0.7149 (tptp) REVERT: B 358 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.6910 (ptmm) REVERT: B 398 THR cc_start: 0.8410 (t) cc_final: 0.8081 (m) REVERT: B 418 LYS cc_start: 0.8215 (mtmt) cc_final: 0.7781 (pttt) REVERT: B 618 ARG cc_start: 0.8703 (mtt180) cc_final: 0.8405 (mtt-85) REVERT: B 700 TYR cc_start: 0.8412 (m-80) cc_final: 0.8122 (m-80) REVERT: C 238 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6468 (mm) REVERT: C 247 GLN cc_start: 0.7215 (tp40) cc_final: 0.6414 (mm-40) REVERT: C 547 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6674 (tp30) REVERT: C 794 MET cc_start: 0.7316 (mtm) cc_final: 0.7006 (mtm) outliers start: 36 outliers final: 23 residues processed: 186 average time/residue: 0.4619 time to fit residues: 97.9014 Evaluate side-chains 172 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 787 SER Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 812 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 24 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN C 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142471 restraints weight = 15062.393| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.13 r_work: 0.3711 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15705 Z= 0.197 Angle : 0.606 9.426 21333 Z= 0.340 Chirality : 0.048 0.167 2481 Planarity : 0.004 0.042 2748 Dihedral : 5.751 29.677 2169 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.30 % Favored : 95.55 % Rotamer: Outliers : 2.61 % Allowed : 14.06 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.18), residues: 1998 helix: 0.10 (0.56), residues: 84 sheet: -0.29 (0.18), residues: 762 loop : -0.62 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 320 TYR 0.017 0.002 TYR B 496 PHE 0.017 0.002 PHE A 370 TRP 0.009 0.001 TRP C 586 HIS 0.005 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00433 (15705) covalent geometry : angle 0.60608 (21333) hydrogen bonds : bond 0.04058 ( 361) hydrogen bonds : angle 5.49616 ( 981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 0.583 Fit side-chains REVERT: A 284 THR cc_start: 0.8211 (p) cc_final: 0.7847 (p) REVERT: A 358 LYS cc_start: 0.7829 (ptpt) cc_final: 0.7161 (tptp) REVERT: B 358 LYS cc_start: 0.7508 (OUTLIER) cc_final: 0.6803 (ptmm) REVERT: B 418 LYS cc_start: 0.8238 (mtmt) cc_final: 0.7970 (pttt) REVERT: B 618 ARG cc_start: 0.8734 (mtt180) cc_final: 0.8526 (mtt-85) REVERT: B 700 TYR cc_start: 0.8465 (m-80) cc_final: 0.8187 (m-80) REVERT: C 238 ILE cc_start: 0.6960 (OUTLIER) cc_final: 0.6567 (mm) REVERT: C 247 GLN cc_start: 0.7096 (tp40) cc_final: 0.6377 (mm-40) REVERT: C 358 LYS cc_start: 0.7135 (ptpt) cc_final: 0.6510 (ptmt) REVERT: C 547 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6735 (tp30) REVERT: C 713 ARG cc_start: 0.8322 (ttt-90) cc_final: 0.8089 (ttp80) REVERT: C 794 MET cc_start: 0.7300 (mtm) cc_final: 0.6999 (mtm) REVERT: C 796 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6684 (m-40) outliers start: 46 outliers final: 30 residues processed: 177 average time/residue: 0.4827 time to fit residues: 96.8913 Evaluate side-chains 174 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 796 ASN Chi-restraints excluded: chain C residue 812 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 117 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 162 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.143945 restraints weight = 14873.138| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.13 r_work: 0.3734 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15705 Z= 0.146 Angle : 0.548 9.012 21333 Z= 0.309 Chirality : 0.047 0.174 2481 Planarity : 0.003 0.039 2748 Dihedral : 5.568 28.184 2169 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.15 % Allowed : 14.80 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.18), residues: 1998 helix: 0.18 (0.57), residues: 84 sheet: -0.27 (0.18), residues: 762 loop : -0.63 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 321 TYR 0.015 0.002 TYR C 520 PHE 0.016 0.002 PHE A 370 TRP 0.007 0.001 TRP A 556 HIS 0.005 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00315 (15705) covalent geometry : angle 0.54829 (21333) hydrogen bonds : bond 0.03600 ( 361) hydrogen bonds : angle 5.35212 ( 981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 142 time to evaluate : 0.546 Fit side-chains REVERT: A 284 THR cc_start: 0.8201 (p) cc_final: 0.7833 (p) REVERT: A 358 LYS cc_start: 0.7864 (ptpt) cc_final: 0.7206 (tptp) REVERT: B 418 LYS cc_start: 0.8261 (mtmt) cc_final: 0.8025 (pttt) REVERT: B 618 ARG cc_start: 0.8712 (mtt180) cc_final: 0.8506 (mtt-85) REVERT: B 700 TYR cc_start: 0.8443 (m-80) cc_final: 0.8144 (m-80) REVERT: C 238 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6371 (mm) REVERT: C 247 GLN cc_start: 0.7054 (tp40) cc_final: 0.6272 (mm-40) REVERT: C 358 LYS cc_start: 0.7126 (ptpt) cc_final: 0.6517 (pttt) REVERT: C 547 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6747 (tp30) REVERT: C 794 MET cc_start: 0.7303 (mtm) cc_final: 0.6997 (mtm) outliers start: 38 outliers final: 30 residues processed: 170 average time/residue: 0.4869 time to fit residues: 94.1891 Evaluate side-chains 171 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 812 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 37 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 166 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.163164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141544 restraints weight = 14979.727| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.13 r_work: 0.3704 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15705 Z= 0.205 Angle : 0.620 9.783 21333 Z= 0.348 Chirality : 0.049 0.194 2481 Planarity : 0.004 0.044 2748 Dihedral : 5.848 29.509 2169 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.65 % Favored : 95.20 % Rotamer: Outliers : 2.10 % Allowed : 14.91 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.18), residues: 1998 helix: 0.05 (0.56), residues: 84 sheet: -0.33 (0.19), residues: 756 loop : -0.70 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 320 TYR 0.017 0.002 TYR B 496 PHE 0.018 0.002 PHE C 734 TRP 0.010 0.002 TRP C 586 HIS 0.004 0.001 HIS C 614 Details of bonding type rmsd covalent geometry : bond 0.00451 (15705) covalent geometry : angle 0.62039 (21333) hydrogen bonds : bond 0.04180 ( 361) hydrogen bonds : angle 5.62801 ( 981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3996 Ramachandran restraints generated. 1998 Oldfield, 0 Emsley, 1998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 0.472 Fit side-chains REVERT: A 284 THR cc_start: 0.8128 (p) cc_final: 0.7755 (p) REVERT: A 358 LYS cc_start: 0.8002 (ptpt) cc_final: 0.7283 (tttm) REVERT: B 418 LYS cc_start: 0.8299 (mtmt) cc_final: 0.8073 (pttt) REVERT: B 618 ARG cc_start: 0.8725 (mtt180) cc_final: 0.8467 (mtt-85) REVERT: B 700 TYR cc_start: 0.8474 (m-80) cc_final: 0.8193 (m-80) REVERT: C 238 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6390 (mm) REVERT: C 247 GLN cc_start: 0.7066 (tp40) cc_final: 0.6371 (mm-40) REVERT: C 358 LYS cc_start: 0.7212 (ptpt) cc_final: 0.6589 (ptmt) REVERT: C 547 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6735 (tp30) REVERT: C 794 MET cc_start: 0.7296 (mtm) cc_final: 0.6982 (mtm) outliers start: 37 outliers final: 30 residues processed: 174 average time/residue: 0.4950 time to fit residues: 97.4616 Evaluate side-chains 171 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 857 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 248 GLU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 812 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 134 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 456 GLN ** B 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.160401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138556 restraints weight = 15060.632| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.11 r_work: 0.3678 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 15705 Z= 0.291 Angle : 0.728 11.126 21333 Z= 0.406 Chirality : 0.053 0.226 2481 Planarity : 0.005 0.058 2748 Dihedral : 6.212 31.196 2169 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.11 % Favored : 94.74 % Rotamer: Outliers : 2.44 % Allowed : 14.74 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.18), residues: 1998 helix: -0.31 (0.53), residues: 84 sheet: -0.32 (0.20), residues: 651 loop : -0.87 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 320 TYR 0.021 0.003 TYR C 465 PHE 0.022 0.003 PHE C 734 TRP 0.012 0.002 TRP C 586 HIS 0.004 0.002 HIS B 614 Details of bonding type rmsd covalent geometry : bond 0.00645 (15705) covalent geometry : angle 0.72773 (21333) hydrogen bonds : bond 0.04899 ( 361) hydrogen bonds : angle 5.99562 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5896.96 seconds wall clock time: 101 minutes 30.16 seconds (6090.16 seconds total)