Starting phenix.real_space_refine on Fri Feb 16 17:44:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/02_2024/6qti_4635_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/02_2024/6qti_4635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/02_2024/6qti_4635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/02_2024/6qti_4635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/02_2024/6qti_4635_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/02_2024/6qti_4635_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 22 5.49 5 S 90 5.16 5 C 10296 2.51 5 N 2568 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 650": "NH1" <-> "NH2" Residue "A TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B ARG 734": "NH1" <-> "NH2" Residue "B TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15996 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7620 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain: "B" Number of atoms: 7620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7620 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain: "A" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 362 Unusual residues: {'D12': 1, 'NAD': 1, 'NAP': 1, 'PC1': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 394 Unusual residues: {'D12': 2, 'NAD': 1, 'NAP': 1, 'PC1': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Time building chain proxies: 9.44, per 1000 atoms: 0.59 Number of scatterers: 15996 At special positions: 0 Unit cell: (138.45, 129.93, 126.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 22 15.00 O 3020 8.00 N 2568 7.00 C 10296 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 - 3.50 Amino acid : False - 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: 6.45 Conformation dependent library (CDL) restraints added in 3.1 seconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 49.1% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 60 through 66 Processing helix chain 'A' and resid 118 through 126 removed outlier: 3.904A pdb=" N LYS A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.634A pdb=" N VAL A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.505A pdb=" N GLU A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 338 through 355 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 412 through 422 removed outlier: 3.729A pdb=" N GLU A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 448 removed outlier: 3.799A pdb=" N VAL A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 474 removed outlier: 3.618A pdb=" N VAL A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP A 474 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 501 removed outlier: 3.997A pdb=" N HIS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER A 482 " --> pdb=" O ALA A 479 " (cutoff:3.500A) Proline residue: A 483 - end of helix removed outlier: 3.713A pdb=" N SER A 492 " --> pdb=" O ASN A 489 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 495 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 500 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 501 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 539 removed outlier: 3.607A pdb=" N ALA A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 519 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 571 Proline residue: A 558 - end of helix removed outlier: 4.692A pdb=" N VAL A 563 " --> pdb=" O GLY A 560 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 564 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU A 567 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 568 " --> pdb=" O GLY A 565 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 571 " --> pdb=" O ALA A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.976A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 623 removed outlier: 4.581A pdb=" N GLY A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 647 removed outlier: 3.575A pdb=" N ALA A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 681 Proline residue: A 657 - end of helix removed outlier: 4.048A pdb=" N HIS A 664 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER A 665 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 666 " --> pdb=" O PHE A 663 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 671 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS A 675 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE A 676 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 677 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 680 " --> pdb=" O ALA A 677 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 681 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 721 removed outlier: 3.949A pdb=" N THR A 695 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS A 696 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL A 698 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY A 702 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY A 706 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 710 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER A 711 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY A 712 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 717 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS A 719 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 721 " --> pdb=" O GLY A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 752 removed outlier: 4.128A pdb=" N ILE A 749 " --> pdb=" O SER A 745 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) Proline residue: A 751 - end of helix Processing helix chain 'A' and resid 759 through 780 removed outlier: 3.652A pdb=" N THR A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 809 removed outlier: 4.047A pdb=" N VAL A 794 " --> pdb=" O VAL A 791 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 795 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER A 799 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 802 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 836 removed outlier: 3.733A pdb=" N ILE A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 871 through 880 removed outlier: 3.518A pdb=" N GLU A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 898 through 910 removed outlier: 3.579A pdb=" N ASP A 903 " --> pdb=" O TYR A 899 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 937 Processing helix chain 'A' and resid 941 through 943 No H-bonds generated for 'chain 'A' and resid 941 through 943' Processing helix chain 'A' and resid 947 through 950 No H-bonds generated for 'chain 'A' and resid 947 through 950' Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.868A pdb=" N GLU A 975 " --> pdb=" O ALA A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing helix chain 'A' and resid 1026 through 1041 Processing helix chain 'B' and resid 33 through 37 removed outlier: 3.893A pdb=" N GLN B 37 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 74 through 77 No H-bonds generated for 'chain 'B' and resid 74 through 77' Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.952A pdb=" N GLU B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.581A pdb=" N LYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 291 No H-bonds generated for 'chain 'B' and resid 288 through 291' Processing helix chain 'B' and resid 334 through 353 removed outlier: 3.799A pdb=" N ALA B 338 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR B 339 " --> pdb=" O ARG B 336 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B 341 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 344 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 345 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 351 " --> pdb=" O ASN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 383 Processing helix chain 'B' and resid 412 through 420 removed outlier: 3.991A pdb=" N GLU B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 448 removed outlier: 3.752A pdb=" N THR B 429 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 473 removed outlier: 3.632A pdb=" N VAL B 473 " --> pdb=" O GLY B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 502 removed outlier: 4.108A pdb=" N HIS B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER B 482 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Proline residue: B 483 - end of helix removed outlier: 3.650A pdb=" N SER B 492 " --> pdb=" O ASN B 489 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 495 " --> pdb=" O SER B 492 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 500 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 501 " --> pdb=" O GLY B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 539 Processing helix chain 'B' and resid 552 through 570 Proline residue: B 558 - end of helix removed outlier: 5.198A pdb=" N VAL B 563 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY B 564 " --> pdb=" O THR B 561 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 567 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA B 568 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 593 removed outlier: 3.757A pdb=" N LEU B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 592 " --> pdb=" O CYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 621 removed outlier: 4.468A pdb=" N GLY B 608 " --> pdb=" O GLY B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 650 removed outlier: 3.633A pdb=" N LYS B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 650 " --> pdb=" O THR B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 681 removed outlier: 3.560A pdb=" N HIS B 664 " --> pdb=" O VAL B 660 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 721 removed outlier: 3.867A pdb=" N ALA B 699 " --> pdb=" O THR B 695 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 752 removed outlier: 4.329A pdb=" N ILE B 749 " --> pdb=" O SER B 745 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) Proline residue: B 751 - end of helix Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.964A pdb=" N ALA B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 810 removed outlier: 3.560A pdb=" N ILE B 792 " --> pdb=" O PRO B 789 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 794 " --> pdb=" O VAL B 791 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU B 795 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER B 799 " --> pdb=" O ASN B 796 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA B 802 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B 808 " --> pdb=" O ALA B 805 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU B 809 " --> pdb=" O GLU B 806 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU B 810 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 836 removed outlier: 3.578A pdb=" N SER B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 871 through 880 Processing helix chain 'B' and resid 890 through 894 Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 929 through 937 Processing helix chain 'B' and resid 947 through 953 removed outlier: 5.216A pdb=" N HIS B 952 " --> pdb=" O ASP B 948 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ASP B 953 " --> pdb=" O GLU B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 969 No H-bonds generated for 'chain 'B' and resid 967 through 969' Processing helix chain 'B' and resid 971 through 975 removed outlier: 4.070A pdb=" N GLU B 975 " --> pdb=" O ALA B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 991 No H-bonds generated for 'chain 'B' and resid 989 through 991' Processing helix chain 'B' and resid 1026 through 1041 Processing sheet with id= A, first strand: chain 'A' and resid 15 through 18 removed outlier: 6.327A pdb=" N ASN A 45 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 18 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 47 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN A 69 " --> pdb=" O VAL A 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 107 through 110 removed outlier: 6.538A pdb=" N THR A 130 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N SER A 110 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LEU A 132 " --> pdb=" O SER A 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 187 through 190 removed outlier: 6.588A pdb=" N ILE A 270 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL A 190 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE A 272 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 299 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N SER A 273 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 301 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N THR A 326 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASP A 302 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 328 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR A 320 " --> pdb=" O HIS A 327 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1019 through 1021 removed outlier: 6.276A pdb=" N VAL A 995 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 960 " --> pdb=" O ILE A 996 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N MET A 998 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 962 " --> pdb=" O MET A 998 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LYS A 914 " --> pdb=" O ILE A 884 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE A 886 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG A 916 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY A 918 " --> pdb=" O PRO A 888 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 15 through 18 removed outlier: 6.330A pdb=" N ASN B 45 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL B 18 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL B 47 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N GLN B 69 " --> pdb=" O VAL B 48 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 107 through 110 removed outlier: 7.158A pdb=" N THR B 130 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N SER B 110 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 132 " --> pdb=" O SER B 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 187 through 190 removed outlier: 6.555A pdb=" N ILE B 270 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N VAL B 190 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 272 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL B 299 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER B 273 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 301 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR B 326 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASP B 302 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE B 328 " --> pdb=" O ASP B 302 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 1019 through 1023 removed outlier: 6.123A pdb=" N VAL B 995 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B1022 " --> pdb=" O VAL B 995 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 997 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS B 914 " --> pdb=" O ILE B 884 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 886 " --> pdb=" O LYS B 914 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG B 916 " --> pdb=" O ILE B 886 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLY B 918 " --> pdb=" O PRO B 888 " (cutoff:3.500A) 631 hydrogen bonds defined for protein. 1539 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: 4.74 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2662 1.32 - 1.44: 3779 1.44 - 1.57: 9631 1.57 - 1.69: 43 1.69 - 1.81: 160 Bond restraints: 16275 Sorted by residual: bond pdb=" O2B NAP B1102 " pdb=" P2B NAP B1102 " ideal model delta sigma weight residual 1.736 1.607 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" O2B NAP A1101 " pdb=" P2B NAP A1101 " ideal model delta sigma weight residual 1.736 1.610 0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C TYR A 683 " pdb=" N PRO A 684 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.19e+01 bond pdb=" O3 NAD B1103 " pdb=" PA NAD B1103 " ideal model delta sigma weight residual 1.653 1.589 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 NAD A1102 " pdb=" PA NAD A1102 " ideal model delta sigma weight residual 1.653 1.591 0.062 2.00e-02 2.50e+03 9.72e+00 ... (remaining 16270 not shown) Histogram of bond angle deviations from ideal: 95.86 - 103.62: 287 103.62 - 111.38: 6713 111.38 - 119.14: 6876 119.14 - 126.90: 7984 126.90 - 134.66: 172 Bond angle restraints: 22032 Sorted by residual: angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 112.96 105.51 7.45 1.00e+00 1.00e+00 5.56e+01 angle pdb=" N VAL B 36 " pdb=" CA VAL B 36 " pdb=" C VAL B 36 " ideal model delta sigma weight residual 112.96 107.04 5.92 1.00e+00 1.00e+00 3.50e+01 angle pdb=" C GLN B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ILE A 579 " pdb=" CA ILE A 579 " pdb=" C ILE A 579 " ideal model delta sigma weight residual 112.96 108.17 4.79 1.00e+00 1.00e+00 2.29e+01 angle pdb=" C ALA B 38 " pdb=" N LEU B 39 " pdb=" CA LEU B 39 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 ... (remaining 22027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 9270 17.00 - 34.01: 509 34.01 - 51.01: 143 51.01 - 68.01: 65 68.01 - 85.01: 28 Dihedral angle restraints: 10015 sinusoidal: 4177 harmonic: 5838 Sorted by residual: dihedral pdb=" CA GLY B 850 " pdb=" C GLY B 850 " pdb=" N THR B 851 " pdb=" CA THR B 851 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLN A 37 " pdb=" C GLN A 37 " pdb=" N ALA A 38 " pdb=" CA ALA A 38 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ALA A 836 " pdb=" C ALA A 836 " pdb=" N MET A 837 " pdb=" CA MET A 837 " ideal model delta harmonic sigma weight residual 180.00 156.77 23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 10012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2180 0.083 - 0.166: 342 0.166 - 0.248: 26 0.248 - 0.331: 1 0.331 - 0.414: 1 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CB ILE B 9 " pdb=" CA ILE B 9 " pdb=" CG1 ILE B 9 " pdb=" CG2 ILE B 9 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA PHE B 365 " pdb=" N PHE B 365 " pdb=" C PHE B 365 " pdb=" CB PHE B 365 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ASP B 361 " pdb=" N ASP B 361 " pdb=" C ASP B 361 " pdb=" CB ASP B 361 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2547 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 365 " 0.014 2.00e-02 2.50e+03 2.10e-02 7.74e+00 pdb=" CG PHE B 365 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 365 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 365 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 365 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 365 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 365 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 805 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ALA A 805 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA A 805 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU A 806 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 920 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 921 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 921 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 921 " -0.034 5.00e-02 4.00e+02 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4352 2.81 - 3.33: 14382 3.33 - 3.86: 25817 3.86 - 4.38: 30631 4.38 - 4.90: 52635 Nonbonded interactions: 127817 Sorted by model distance: nonbonded pdb=" OE1 GLU B 306 " pdb=" OG1 THR B 331 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR B 495 " pdb=" OG SER B 524 " model vdw 2.292 2.440 nonbonded pdb=" O ASP B 953 " pdb=" OG1 THR B 957 " model vdw 2.298 2.440 nonbonded pdb=" OG1 THR B 411 " pdb=" O GLN B 974 " model vdw 2.300 2.440 nonbonded pdb=" OD2 ASP A 119 " pdb=" NZ LYS A 123 " model vdw 2.316 2.520 ... (remaining 127812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 1042 or resid 1104 through 1105 or resid 1109)) selection = (chain 'B' and (resid 5 through 1042 or (resid 1104 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C3A or name C3B or name C3C or name C3D or name C3E \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P )) or (resid 1105 and (name N or name C1 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C \ 22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or na \ me C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C3A or name C3B or name C3C or name C3D or nam \ e C3E or name C3F or name C3G or name C3H or name C3I or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ )) or (resid 1109 and (name N or name C1 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C2A or name \ C2B or name C2C or name C3 or name C31 or name C32 or name C33 or name C34 or na \ me C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 o \ r name O21 or name O22 or name O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 1.510 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 45.090 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.007 0.129 16275 Z= 0.458 Angle : 1.010 11.431 22032 Z= 0.509 Chirality : 0.058 0.414 2550 Planarity : 0.008 0.061 2730 Dihedral : 13.499 85.014 6319 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.15), residues: 2072 helix: -2.29 (0.11), residues: 1080 sheet: -1.52 (0.37), residues: 186 loop : -2.80 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 801 HIS 0.019 0.003 HIS B 481 PHE 0.048 0.003 PHE B 365 TYR 0.025 0.003 TYR B 330 ARG 0.006 0.001 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.827 Fit side-chains REVERT: A 20 LYS cc_start: 0.8939 (tttp) cc_final: 0.8666 (ttpp) REVERT: A 74 LYS cc_start: 0.8766 (tmtp) cc_final: 0.8410 (tttm) REVERT: A 100 ASP cc_start: 0.8683 (m-30) cc_final: 0.8448 (m-30) REVERT: A 288 LYS cc_start: 0.8570 (ptmm) cc_final: 0.8228 (ptmm) REVERT: A 376 MET cc_start: 0.8797 (mmm) cc_final: 0.8524 (mmt) REVERT: A 427 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7670 (tpp-160) REVERT: A 476 VAL cc_start: 0.9136 (m) cc_final: 0.8874 (t) REVERT: A 501 VAL cc_start: 0.9178 (t) cc_final: 0.8784 (m) REVERT: A 503 MET cc_start: 0.8983 (ttt) cc_final: 0.8741 (ttt) REVERT: A 628 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8500 (mp0) REVERT: A 754 MET cc_start: 0.6712 (mpt) cc_final: 0.6446 (ptt) REVERT: A 903 ASP cc_start: 0.8614 (t70) cc_final: 0.8233 (m-30) REVERT: A 906 LYS cc_start: 0.8790 (tttt) cc_final: 0.8575 (ttpp) REVERT: A 1038 ARG cc_start: 0.7366 (ttm110) cc_final: 0.7149 (ttp80) REVERT: B 74 LYS cc_start: 0.9155 (tmtt) cc_final: 0.8806 (mppt) REVERT: B 127 ARG cc_start: 0.7596 (tpm-80) cc_final: 0.7372 (mmt180) REVERT: B 414 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6882 (mt-10) REVERT: B 681 ILE cc_start: 0.8976 (tt) cc_final: 0.8644 (pp) REVERT: B 858 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7234 (pptt) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 1.2258 time to fit residues: 408.5851 Evaluate side-chains 182 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 128 ASN A 287 ASN A 310 ASN A 327 HIS A 403 GLN A 552 ASN A 693 ASN B 62 HIS ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1034 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16275 Z= 0.234 Angle : 0.583 6.025 22032 Z= 0.294 Chirality : 0.042 0.165 2550 Planarity : 0.006 0.053 2730 Dihedral : 12.699 85.735 2921 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.93 % Allowed : 10.36 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2072 helix: -0.49 (0.15), residues: 1083 sheet: -1.12 (0.38), residues: 186 loop : -2.35 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 801 HIS 0.009 0.001 HIS B 481 PHE 0.030 0.002 PHE B 365 TYR 0.014 0.001 TYR B 941 ARG 0.004 0.000 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 212 time to evaluate : 1.794 Fit side-chains REVERT: A 20 LYS cc_start: 0.8881 (tttp) cc_final: 0.8587 (ttpp) REVERT: A 74 LYS cc_start: 0.8789 (tmtp) cc_final: 0.8415 (mttt) REVERT: A 100 ASP cc_start: 0.8671 (m-30) cc_final: 0.8447 (m-30) REVERT: A 249 MET cc_start: 0.8418 (mmt) cc_final: 0.8169 (mmp) REVERT: A 288 LYS cc_start: 0.8620 (ptmm) cc_final: 0.8258 (ptmm) REVERT: A 427 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7536 (tpt170) REVERT: A 788 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8746 (tpt) REVERT: A 833 MET cc_start: 0.8819 (ttm) cc_final: 0.8598 (mtp) REVERT: A 877 MET cc_start: 0.8321 (ttp) cc_final: 0.7976 (ttp) REVERT: A 903 ASP cc_start: 0.8661 (t70) cc_final: 0.8244 (m-30) REVERT: B 74 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8745 (mppt) REVERT: B 414 GLU cc_start: 0.7291 (mm-30) cc_final: 0.6643 (mt-10) REVERT: B 833 MET cc_start: 0.8885 (ttm) cc_final: 0.7915 (tpp) REVERT: B 858 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7337 (pptt) outliers start: 47 outliers final: 14 residues processed: 241 average time/residue: 1.1522 time to fit residues: 310.9935 Evaluate side-chains 191 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 202 optimal weight: 20.0000 chunk 166 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 144 GLN A 327 HIS A 457 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 796 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16275 Z= 0.222 Angle : 0.554 8.021 22032 Z= 0.278 Chirality : 0.042 0.167 2550 Planarity : 0.005 0.045 2730 Dihedral : 12.206 86.053 2921 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.31 % Allowed : 12.23 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2072 helix: 0.16 (0.16), residues: 1086 sheet: -0.88 (0.39), residues: 186 loop : -2.14 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 801 HIS 0.008 0.001 HIS A 481 PHE 0.052 0.002 PHE B 365 TYR 0.012 0.001 TYR A 11 ARG 0.003 0.000 ARG A1038 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 2.032 Fit side-chains REVERT: A 20 LYS cc_start: 0.8867 (tttp) cc_final: 0.8565 (ttpp) REVERT: A 74 LYS cc_start: 0.8809 (tmtp) cc_final: 0.8389 (mttt) REVERT: A 100 ASP cc_start: 0.8699 (m-30) cc_final: 0.8464 (m-30) REVERT: A 197 LEU cc_start: 0.8951 (mt) cc_final: 0.8740 (mp) REVERT: A 288 LYS cc_start: 0.8537 (ptmm) cc_final: 0.8284 (ptmm) REVERT: A 403 GLN cc_start: 0.2830 (OUTLIER) cc_final: 0.1386 (tp40) REVERT: A 416 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: A 427 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.7552 (mmt180) REVERT: A 602 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7645 (mtm180) REVERT: A 788 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8575 (tpt) REVERT: A 833 MET cc_start: 0.8822 (ttm) cc_final: 0.8617 (mtp) REVERT: A 877 MET cc_start: 0.8310 (ttp) cc_final: 0.7918 (ttp) REVERT: A 903 ASP cc_start: 0.8714 (t70) cc_final: 0.8222 (m-30) REVERT: A 1023 LEU cc_start: 0.8973 (mt) cc_final: 0.8655 (mm) REVERT: B 74 LYS cc_start: 0.9168 (tmtt) cc_final: 0.8835 (mppt) REVERT: B 414 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6635 (mt-10) REVERT: B 602 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7601 (mpp-170) REVERT: B 788 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8340 (tpt) REVERT: B 833 MET cc_start: 0.8900 (ttm) cc_final: 0.7833 (tpp) REVERT: B 858 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7288 (pptt) outliers start: 53 outliers final: 17 residues processed: 226 average time/residue: 1.2309 time to fit residues: 310.6884 Evaluate side-chains 202 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 788 MET Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 0.0670 chunk 20 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 188 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 327 HIS ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16275 Z= 0.185 Angle : 0.526 6.359 22032 Z= 0.265 Chirality : 0.041 0.158 2550 Planarity : 0.004 0.043 2730 Dihedral : 11.786 87.130 2921 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.06 % Allowed : 13.55 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 2072 helix: 0.56 (0.16), residues: 1086 sheet: -0.63 (0.40), residues: 184 loop : -1.99 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 801 HIS 0.007 0.001 HIS B 866 PHE 0.042 0.001 PHE B 365 TYR 0.031 0.001 TYR B 571 ARG 0.002 0.000 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 186 time to evaluate : 1.632 Fit side-chains REVERT: A 20 LYS cc_start: 0.8855 (tttp) cc_final: 0.8555 (ttpp) REVERT: A 74 LYS cc_start: 0.8859 (tmtp) cc_final: 0.8408 (mttt) REVERT: A 100 ASP cc_start: 0.8697 (m-30) cc_final: 0.8450 (m-30) REVERT: A 197 LEU cc_start: 0.8970 (mt) cc_final: 0.8760 (mp) REVERT: A 221 GLU cc_start: 0.8319 (mp0) cc_final: 0.7994 (mp0) REVERT: A 288 LYS cc_start: 0.8528 (ptmm) cc_final: 0.8255 (ptmm) REVERT: A 403 GLN cc_start: 0.2828 (OUTLIER) cc_final: 0.1406 (tp40) REVERT: A 416 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: A 427 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7508 (mmt180) REVERT: A 602 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7641 (mtm180) REVERT: A 788 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8491 (tpt) REVERT: A 877 MET cc_start: 0.8277 (ttp) cc_final: 0.8012 (ttp) REVERT: A 903 ASP cc_start: 0.8692 (t70) cc_final: 0.8223 (m-30) REVERT: A 1023 LEU cc_start: 0.8961 (mt) cc_final: 0.8661 (mm) REVERT: B 74 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8838 (mppt) REVERT: B 337 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8570 (mtt) REVERT: B 414 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6784 (mt-10) REVERT: B 602 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7573 (mpp-170) REVERT: B 681 ILE cc_start: 0.8809 (tt) cc_final: 0.8526 (pt) REVERT: B 833 MET cc_start: 0.8908 (ttm) cc_final: 0.7850 (tpp) REVERT: B 858 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7261 (pptt) outliers start: 49 outliers final: 19 residues processed: 215 average time/residue: 1.1785 time to fit residues: 282.9550 Evaluate side-chains 203 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 178 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 327 HIS A 552 ASN B 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 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 : 0.004 0.036 16275 Z= 0.233 Angle : 0.544 6.051 22032 Z= 0.272 Chirality : 0.042 0.169 2550 Planarity : 0.004 0.041 2730 Dihedral : 11.898 89.175 2921 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.37 % Allowed : 13.80 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 2072 helix: 0.66 (0.16), residues: 1091 sheet: -0.55 (0.40), residues: 183 loop : -1.87 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 474 HIS 0.007 0.001 HIS B 866 PHE 0.035 0.001 PHE B 365 TYR 0.022 0.001 TYR B 571 ARG 0.003 0.000 ARG A1038 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 179 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8795 (tttp) cc_final: 0.8533 (ttpp) REVERT: A 74 LYS cc_start: 0.8864 (tmtp) cc_final: 0.8410 (mttt) REVERT: A 100 ASP cc_start: 0.8688 (m-30) cc_final: 0.8438 (m-30) REVERT: A 144 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8131 (mp10) REVERT: A 197 LEU cc_start: 0.8982 (mt) cc_final: 0.8763 (mp) REVERT: A 223 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8714 (m-80) REVERT: A 288 LYS cc_start: 0.8523 (ptmm) cc_final: 0.8275 (ptmm) REVERT: A 403 GLN cc_start: 0.2795 (OUTLIER) cc_final: 0.1394 (tp40) REVERT: A 416 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: A 427 ARG cc_start: 0.7864 (ttp-170) cc_final: 0.7521 (mmt180) REVERT: A 788 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8765 (tpt) REVERT: A 877 MET cc_start: 0.8229 (ttp) cc_final: 0.7958 (ttp) REVERT: A 903 ASP cc_start: 0.8592 (t70) cc_final: 0.8254 (m-30) REVERT: A 1023 LEU cc_start: 0.8962 (mt) cc_final: 0.8643 (mm) REVERT: B 74 LYS cc_start: 0.9211 (tmtt) cc_final: 0.8864 (mppt) REVERT: B 414 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6717 (mt-10) REVERT: B 418 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: B 602 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7578 (mpp-170) REVERT: B 858 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7248 (pptt) REVERT: B 893 CYS cc_start: 0.8519 (m) cc_final: 0.8087 (t) outliers start: 54 outliers final: 28 residues processed: 215 average time/residue: 1.1750 time to fit residues: 284.1713 Evaluate side-chains 209 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 0.0570 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 552 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16275 Z= 0.207 Angle : 0.530 6.013 22032 Z= 0.266 Chirality : 0.042 0.225 2550 Planarity : 0.004 0.040 2730 Dihedral : 11.833 89.175 2921 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.06 % Allowed : 14.92 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 2072 helix: 0.79 (0.16), residues: 1094 sheet: -0.30 (0.42), residues: 177 loop : -1.79 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 474 HIS 0.006 0.001 HIS B 866 PHE 0.032 0.001 PHE B 365 TYR 0.019 0.001 TYR B 571 ARG 0.002 0.000 ARG A1038 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 1.990 Fit side-chains revert: symmetry clash REVERT: A 20 LYS cc_start: 0.8777 (tttp) cc_final: 0.8516 (ttpp) REVERT: A 74 LYS cc_start: 0.8870 (tmtp) cc_final: 0.8409 (mttt) REVERT: A 100 ASP cc_start: 0.8680 (m-30) cc_final: 0.8432 (m-30) REVERT: A 144 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8152 (mp10) REVERT: A 197 LEU cc_start: 0.8985 (mt) cc_final: 0.8765 (mp) REVERT: A 223 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: A 288 LYS cc_start: 0.8510 (ptmm) cc_final: 0.8263 (ptmm) REVERT: A 403 GLN cc_start: 0.2788 (OUTLIER) cc_final: 0.1380 (tp40) REVERT: A 416 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6596 (mp0) REVERT: A 427 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7512 (mmt180) REVERT: A 501 VAL cc_start: 0.9074 (t) cc_final: 0.8713 (m) REVERT: A 788 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8659 (tpt) REVERT: A 877 MET cc_start: 0.8214 (ttp) cc_final: 0.7967 (ttp) REVERT: A 903 ASP cc_start: 0.8641 (t70) cc_final: 0.8279 (m-30) REVERT: A 1023 LEU cc_start: 0.8958 (mt) cc_final: 0.8633 (mm) REVERT: B 74 LYS cc_start: 0.9194 (tmtt) cc_final: 0.8855 (mppt) REVERT: B 337 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8521 (mtt) REVERT: B 376 MET cc_start: 0.8526 (tpp) cc_final: 0.8195 (tpt) REVERT: B 414 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6707 (mt-10) REVERT: B 602 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7552 (mpp-170) REVERT: B 658 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8509 (mt0) REVERT: B 681 ILE cc_start: 0.8817 (tt) cc_final: 0.8588 (pt) REVERT: B 858 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7252 (pptt) REVERT: B 871 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7932 (mt) REVERT: B 893 CYS cc_start: 0.8546 (m) cc_final: 0.8153 (t) outliers start: 49 outliers final: 26 residues processed: 210 average time/residue: 1.1648 time to fit residues: 273.9287 Evaluate side-chains 202 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 124 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 327 HIS A 489 ASN A 552 ASN B 340 GLN B 866 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16275 Z= 0.259 Angle : 0.557 8.390 22032 Z= 0.278 Chirality : 0.043 0.210 2550 Planarity : 0.004 0.042 2730 Dihedral : 11.966 87.398 2921 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.37 % Allowed : 14.98 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 2072 helix: 0.78 (0.16), residues: 1094 sheet: -0.24 (0.42), residues: 177 loop : -1.73 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 474 HIS 0.008 0.001 HIS B 866 PHE 0.030 0.001 PHE B 365 TYR 0.016 0.001 TYR B 571 ARG 0.003 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 1.873 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8887 (tmtp) cc_final: 0.8405 (mttt) REVERT: A 100 ASP cc_start: 0.8650 (m-30) cc_final: 0.8403 (m-30) REVERT: A 144 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8164 (mp10) REVERT: A 197 LEU cc_start: 0.8991 (mt) cc_final: 0.8772 (mp) REVERT: A 223 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8728 (m-80) REVERT: A 288 LYS cc_start: 0.8524 (ptmm) cc_final: 0.8282 (ptmm) REVERT: A 403 GLN cc_start: 0.2920 (OUTLIER) cc_final: 0.1415 (tp40) REVERT: A 416 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: A 427 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7524 (mmt180) REVERT: A 788 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8661 (tpt) REVERT: A 877 MET cc_start: 0.8154 (ttp) cc_final: 0.7927 (ttp) REVERT: A 903 ASP cc_start: 0.8668 (t70) cc_final: 0.8281 (m-30) REVERT: B 74 LYS cc_start: 0.9202 (tmtt) cc_final: 0.8865 (mppt) REVERT: B 332 ASP cc_start: 0.8930 (p0) cc_final: 0.8546 (p0) REVERT: B 376 MET cc_start: 0.8537 (tpp) cc_final: 0.8191 (tpt) REVERT: B 403 GLN cc_start: 0.1549 (OUTLIER) cc_final: 0.1329 (tt0) REVERT: B 414 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6641 (mt-10) REVERT: B 602 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7593 (mpp-170) REVERT: B 681 ILE cc_start: 0.8829 (tt) cc_final: 0.8565 (pt) REVERT: B 858 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7281 (pptt) REVERT: B 893 CYS cc_start: 0.8554 (m) cc_final: 0.8169 (t) outliers start: 54 outliers final: 32 residues processed: 213 average time/residue: 1.1661 time to fit residues: 281.0336 Evaluate side-chains 202 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 956 ASP Chi-restraints excluded: chain B residue 1002 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 38 optimal weight: 8.9990 chunk 126 optimal weight: 0.0570 chunk 135 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN B 866 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16275 Z= 0.254 Angle : 0.561 7.891 22032 Z= 0.282 Chirality : 0.043 0.210 2550 Planarity : 0.004 0.044 2730 Dihedral : 12.032 87.207 2921 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.00 % Allowed : 15.67 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 2072 helix: 0.84 (0.16), residues: 1088 sheet: -0.20 (0.42), residues: 177 loop : -1.68 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 474 HIS 0.009 0.001 HIS B 866 PHE 0.028 0.001 PHE B 365 TYR 0.011 0.001 TYR B 941 ARG 0.003 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 1.938 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8852 (tmtp) cc_final: 0.8337 (mttt) REVERT: A 144 GLN cc_start: 0.8929 (mm-40) cc_final: 0.8217 (mp10) REVERT: A 197 LEU cc_start: 0.8995 (mt) cc_final: 0.8794 (mp) REVERT: A 223 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8731 (m-80) REVERT: A 288 LYS cc_start: 0.8690 (ptmm) cc_final: 0.8390 (ptmm) REVERT: A 296 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8210 (tt0) REVERT: A 403 GLN cc_start: 0.3131 (OUTLIER) cc_final: 0.1549 (tp40) REVERT: A 416 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6577 (mp0) REVERT: A 427 ARG cc_start: 0.7904 (ttp-170) cc_final: 0.7563 (mmt180) REVERT: A 788 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8638 (tpt) REVERT: A 903 ASP cc_start: 0.8675 (t70) cc_final: 0.8279 (m-30) REVERT: A 956 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.6910 (p0) REVERT: B 74 LYS cc_start: 0.9222 (tmtt) cc_final: 0.8899 (mppt) REVERT: B 332 ASP cc_start: 0.8932 (p0) cc_final: 0.8555 (p0) REVERT: B 376 MET cc_start: 0.8529 (tpp) cc_final: 0.8200 (tpp) REVERT: B 414 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6797 (mt-10) REVERT: B 602 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7594 (mpp-170) REVERT: B 658 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: B 681 ILE cc_start: 0.8826 (tt) cc_final: 0.8556 (pt) REVERT: B 683 TYR cc_start: 0.8397 (t80) cc_final: 0.8115 (t80) REVERT: B 858 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7357 (pptt) REVERT: B 893 CYS cc_start: 0.8720 (m) cc_final: 0.8444 (t) outliers start: 48 outliers final: 26 residues processed: 206 average time/residue: 1.2165 time to fit residues: 280.2601 Evaluate side-chains 197 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 173 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS B 403 GLN B 658 GLN B 866 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16275 Z= 0.360 Angle : 0.623 8.207 22032 Z= 0.311 Chirality : 0.046 0.207 2550 Planarity : 0.005 0.046 2730 Dihedral : 12.403 86.119 2921 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.81 % Allowed : 16.10 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 2072 helix: 0.69 (0.16), residues: 1095 sheet: -0.30 (0.42), residues: 177 loop : -1.66 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 801 HIS 0.014 0.002 HIS B 866 PHE 0.033 0.002 PHE B 393 TYR 0.016 0.002 TYR A 364 ARG 0.004 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 173 time to evaluate : 1.842 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8869 (tmtp) cc_final: 0.8345 (mttt) REVERT: A 197 LEU cc_start: 0.8981 (mt) cc_final: 0.8775 (mp) REVERT: A 223 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8738 (m-80) REVERT: A 288 LYS cc_start: 0.8711 (ptmm) cc_final: 0.8442 (ptmm) REVERT: A 403 GLN cc_start: 0.3289 (OUTLIER) cc_final: 0.1656 (tp40) REVERT: A 416 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: A 427 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7686 (mmt180) REVERT: A 903 ASP cc_start: 0.8691 (t70) cc_final: 0.8288 (m-30) REVERT: A 956 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7104 (p0) REVERT: B 74 LYS cc_start: 0.9261 (tmtt) cc_final: 0.9034 (tptt) REVERT: B 332 ASP cc_start: 0.8945 (p0) cc_final: 0.8591 (p0) REVERT: B 376 MET cc_start: 0.8518 (tpp) cc_final: 0.8167 (tpp) REVERT: B 414 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6786 (mt-10) REVERT: B 602 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7621 (mpp-170) REVERT: B 858 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7262 (pptt) REVERT: B 861 GLU cc_start: 0.7083 (pm20) cc_final: 0.6593 (mp0) REVERT: B 893 CYS cc_start: 0.8631 (m) cc_final: 0.8428 (t) outliers start: 45 outliers final: 31 residues processed: 206 average time/residue: 1.1979 time to fit residues: 277.1561 Evaluate side-chains 200 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 956 ASP Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 772 SER Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 100 optimal weight: 0.0770 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 552 ASN B 42 GLN B 166 ASN B 658 GLN B 866 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16275 Z= 0.135 Angle : 0.510 8.620 22032 Z= 0.258 Chirality : 0.040 0.199 2550 Planarity : 0.004 0.041 2730 Dihedral : 11.710 86.986 2921 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.06 % Allowed : 17.10 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 2072 helix: 1.11 (0.16), residues: 1088 sheet: -0.04 (0.43), residues: 174 loop : -1.57 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 801 HIS 0.009 0.001 HIS B 866 PHE 0.029 0.001 PHE B 365 TYR 0.009 0.001 TYR A 11 ARG 0.003 0.000 ARG A1038 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 1.808 Fit side-chains REVERT: A 74 LYS cc_start: 0.8879 (tmtp) cc_final: 0.8399 (mttt) REVERT: A 144 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8187 (mp10) REVERT: A 197 LEU cc_start: 0.8990 (mt) cc_final: 0.8787 (mp) REVERT: A 288 LYS cc_start: 0.8671 (ptmm) cc_final: 0.8389 (ptmm) REVERT: A 403 GLN cc_start: 0.2978 (OUTLIER) cc_final: 0.1550 (tp40) REVERT: A 416 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: A 427 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7507 (mmt180) REVERT: A 501 VAL cc_start: 0.9030 (t) cc_final: 0.8702 (m) REVERT: A 602 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7711 (mtm180) REVERT: A 903 ASP cc_start: 0.8628 (t70) cc_final: 0.8292 (m-30) REVERT: B 74 LYS cc_start: 0.9277 (tmtt) cc_final: 0.8910 (mppt) REVERT: B 294 MET cc_start: 0.9208 (mtp) cc_final: 0.8887 (mtp) REVERT: B 332 ASP cc_start: 0.8853 (p0) cc_final: 0.8467 (p0) REVERT: B 376 MET cc_start: 0.8408 (tpp) cc_final: 0.8055 (tpp) REVERT: B 414 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6682 (mt-10) REVERT: B 658 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8595 (mt0) REVERT: B 833 MET cc_start: 0.8149 (mtp) cc_final: 0.7374 (mmt) REVERT: B 858 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7293 (pptt) REVERT: B 871 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7918 (mt) outliers start: 33 outliers final: 14 residues processed: 207 average time/residue: 1.1685 time to fit residues: 270.8590 Evaluate side-chains 182 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 658 GLN Chi-restraints excluded: chain B residue 787 ASP Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 871 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 10.0000 chunk 174 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 68 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 552 ASN B 122 ASN B 658 GLN B 866 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.092530 restraints weight = 21268.653| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.79 r_work: 0.2908 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16275 Z= 0.377 Angle : 0.634 12.485 22032 Z= 0.315 Chirality : 0.046 0.213 2550 Planarity : 0.005 0.045 2730 Dihedral : 12.324 86.279 2921 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.06 % Allowed : 17.29 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 2072 helix: 0.81 (0.16), residues: 1098 sheet: -0.25 (0.42), residues: 177 loop : -1.57 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 801 HIS 0.012 0.002 HIS B 866 PHE 0.035 0.002 PHE B 393 TYR 0.016 0.002 TYR A 364 ARG 0.004 0.001 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5402.22 seconds wall clock time: 97 minutes 0.21 seconds (5820.21 seconds total)