Starting phenix.real_space_refine on Sun Nov 17 05:14:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/11_2024/7xs6_33422_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/11_2024/7xs6_33422.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/7xs6_33422/11_2024/7xs6_33422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/11_2024/7xs6_33422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/11_2024/7xs6_33422_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/11_2024/7xs6_33422_neut.cif" } 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= 0.000 sd= 0.006 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 2 5.49 5 S 72 5.16 5 C 8298 2.51 5 N 1926 2.21 5 O 2142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12440 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5917 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 706} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ARG%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 5917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5917 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 706} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ARG%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 270 Unusual residues: {'BGI': 1, 'C14': 9, 'D12': 5, 'HP6': 7} Classifications: {'undetermined': 22} Link IDs: {None: 21} Chain: "A" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 336 Unusual residues: {'0V9': 2, 'BGI': 1, 'C14': 7, 'D12': 5, 'HP6': 7} Classifications: {'undetermined': 22} Link IDs: {None: 21} Time building chain proxies: 7.07, per 1000 atoms: 0.57 Number of scatterers: 12440 At special positions: 0 Unit cell: (115.56, 109.08, 115.56, 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 72 16.00 P 2 15.00 O 2142 8.00 N 1926 7.00 C 8298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2780 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 58.7% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'B' and resid 392 through 403 removed outlier: 3.504A pdb=" N THR B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 458 through 479 removed outlier: 3.670A pdb=" N LYS B 479 " --> pdb=" O TYR B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 removed outlier: 3.656A pdb=" N LYS B 491 " --> pdb=" O ASP B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 506 through 516 Processing helix chain 'B' and resid 578 through 587 Processing helix chain 'B' and resid 588 through 594 Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 636 through 643 removed outlier: 5.890A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 661 Processing helix chain 'B' and resid 661 through 669 removed outlier: 3.514A pdb=" N ASN B 667 " --> pdb=" O THR B 663 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 711 removed outlier: 3.596A pdb=" N ASN B 711 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 715 Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.713A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 722 " --> pdb=" O ARG B 718 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 3.879A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 778 Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.507A pdb=" N PHE B 796 " --> pdb=" O THR B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.563A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 824 " --> pdb=" O THR B 820 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 826 " --> pdb=" O SER B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 855 removed outlier: 3.536A pdb=" N VAL B 836 " --> pdb=" O ASN B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 895 removed outlier: 3.809A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 932 Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.646A pdb=" N THR B 940 " --> pdb=" O TRP B 936 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 936 through 941' Processing helix chain 'B' and resid 942 through 954 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 954 through 963 Processing helix chain 'B' and resid 997 through 1012 removed outlier: 3.922A pdb=" N LEU B1012 " --> pdb=" O TYR B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1059 removed outlier: 3.897A pdb=" N GLY B1034 " --> pdb=" O GLU B1030 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1063 through 1075 Processing helix chain 'B' and resid 1091 through 1130 removed outlier: 4.186A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL B1105 " --> pdb=" O ILE B1101 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B1130 " --> pdb=" O LYS B1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 403 removed outlier: 3.500A pdb=" N THR A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 458 through 479 removed outlier: 3.670A pdb=" N LYS A 479 " --> pdb=" O TYR A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 removed outlier: 3.695A pdb=" N LYS A 491 " --> pdb=" O ASP A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 506 through 516 Processing helix chain 'A' and resid 578 through 587 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.517A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 636 through 643 removed outlier: 5.891A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 658 Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.515A pdb=" N ASN A 667 " --> pdb=" O THR A 663 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 711 removed outlier: 3.589A pdb=" N ASN A 711 " --> pdb=" O PHE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 715 removed outlier: 3.509A pdb=" N ALA A 715 " --> pdb=" O MET A 712 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 712 through 715' Processing helix chain 'A' and resid 718 through 726 removed outlier: 3.619A pdb=" N PHE A 722 " --> pdb=" O ARG A 718 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 3.911A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 778 Processing helix chain 'A' and resid 784 through 807 Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.563A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 855 removed outlier: 3.531A pdb=" N VAL A 836 " --> pdb=" O ASN A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 895 removed outlier: 3.781A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 932 Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.642A pdb=" N THR A 940 " --> pdb=" O TRP A 936 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 936 through 941' Processing helix chain 'A' and resid 942 through 954 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 954 through 963 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.524A pdb=" N VAL A1011 " --> pdb=" O LYS A1007 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A1012 " --> pdb=" O TYR A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1059 removed outlier: 3.712A pdb=" N GLY A1034 " --> pdb=" O GLU A1030 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 Processing helix chain 'A' and resid 1091 through 1130 removed outlier: 4.192A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A1105 " --> pdb=" O ILE A1101 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A1130 " --> pdb=" O LYS A1126 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 385 through 390 removed outlier: 4.632A pdb=" N PHE B 385 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 389 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 629 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 682 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 624 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LYS B 735 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY B 626 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N CYS B 737 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS B 628 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER B 739 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU B 630 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR B 741 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 632 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER B 743 " --> pdb=" O ARG B 632 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 385 through 390 removed outlier: 4.632A pdb=" N PHE B 385 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER B 389 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 678 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 629 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG B 682 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 624 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LYS B 735 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY B 626 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N CYS B 737 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N CYS B 628 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER B 739 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU B 630 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR B 741 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG B 632 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N SER B 743 " --> pdb=" O ARG B 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 527 through 528 removed outlier: 6.289A pdb=" N GLU B 527 " --> pdb=" O ILE A 982 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.612A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 981 through 982 Processing sheet with id=AA6, first strand: chain 'B' and resid 1086 through 1088 Processing sheet with id=AA7, first strand: chain 'A' and resid 385 through 390 removed outlier: 4.636A pdb=" N PHE A 385 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 389 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 453 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 679 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 629 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 682 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 624 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS A 735 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY A 626 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS A 737 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS A 628 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER A 739 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLU A 630 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 741 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG A 632 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER A 743 " --> pdb=" O ARG A 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 385 through 390 removed outlier: 4.636A pdb=" N PHE A 385 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 389 " --> pdb=" O MET A 416 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 453 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 679 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 678 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 629 " --> pdb=" O PHE A 678 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG A 682 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 624 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS A 735 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY A 626 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N CYS A 737 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N CYS A 628 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER A 739 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLU A 630 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 741 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG A 632 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER A 743 " --> pdb=" O ARG A 632 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.613A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1929 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: 4.65 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1836 1.30 - 1.43: 3403 1.43 - 1.55: 7337 1.55 - 1.68: 8 1.68 - 1.81: 112 Bond restraints: 12696 Sorted by residual: bond pdb=" C18 BGI A2022 " pdb=" C19 BGI A2022 " ideal model delta sigma weight residual 1.526 1.243 0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C18 BGI B1222 " pdb=" C19 BGI B1222 " ideal model delta sigma weight residual 1.526 1.243 0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C06 BGI A2022 " pdb=" N05 BGI A2022 " ideal model delta sigma weight residual 1.326 1.485 -0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" C06 BGI B1222 " pdb=" N05 BGI B1222 " ideal model delta sigma weight residual 1.326 1.484 -0.158 2.00e-02 2.50e+03 6.25e+01 bond pdb=" C04 BGI B1222 " pdb=" N05 BGI B1222 " ideal model delta sigma weight residual 1.326 1.481 -0.155 2.00e-02 2.50e+03 5.97e+01 ... (remaining 12691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 16112 1.63 - 3.25: 760 3.25 - 4.88: 80 4.88 - 6.50: 24 6.50 - 8.13: 16 Bond angle restraints: 16992 Sorted by residual: angle pdb=" N VAL B 996 " pdb=" CA VAL B 996 " pdb=" C VAL B 996 " ideal model delta sigma weight residual 113.71 108.16 5.55 9.50e-01 1.11e+00 3.42e+01 angle pdb=" N VAL A 996 " pdb=" CA VAL A 996 " pdb=" C VAL A 996 " ideal model delta sigma weight residual 113.71 108.19 5.52 9.50e-01 1.11e+00 3.38e+01 angle pdb=" N LYS B1031 " pdb=" CA LYS B1031 " pdb=" C LYS B1031 " ideal model delta sigma weight residual 113.41 106.88 6.53 1.22e+00 6.72e-01 2.86e+01 angle pdb=" N VAL A 915 " pdb=" CA VAL A 915 " pdb=" C VAL A 915 " ideal model delta sigma weight residual 111.91 107.44 4.47 8.90e-01 1.26e+00 2.53e+01 angle pdb=" N VAL B 915 " pdb=" CA VAL B 915 " pdb=" C VAL B 915 " ideal model delta sigma weight residual 111.91 107.57 4.34 8.90e-01 1.26e+00 2.38e+01 ... (remaining 16987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 7265 24.70 - 49.41: 315 49.41 - 74.11: 38 74.11 - 98.81: 34 98.81 - 123.52: 8 Dihedral angle restraints: 7660 sinusoidal: 3358 harmonic: 4302 Sorted by residual: dihedral pdb=" C37 0V9 A2001 " pdb=" C38 0V9 A2001 " pdb=" C39 0V9 A2001 " pdb=" C40 0V9 A2001 " ideal model delta sinusoidal sigma weight residual -164.85 -41.33 -123.52 1 3.00e+01 1.11e-03 1.66e+01 dihedral pdb=" C1 0V9 A2001 " pdb=" O3P 0V9 A2001 " pdb=" P 0V9 A2001 " pdb=" O4P 0V9 A2001 " ideal model delta sinusoidal sigma weight residual -67.07 -174.72 107.65 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C37 0V9 A2002 " pdb=" C38 0V9 A2002 " pdb=" C39 0V9 A2002 " pdb=" C40 0V9 A2002 " ideal model delta sinusoidal sigma weight residual -164.85 -57.47 -107.38 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 7657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1751 0.081 - 0.161: 109 0.161 - 0.242: 2 0.242 - 0.322: 0 0.322 - 0.403: 2 Chirality restraints: 1864 Sorted by residual: chirality pdb=" C18 BGI B1222 " pdb=" C17 BGI B1222 " pdb=" C19 BGI B1222 " pdb=" O31 BGI B1222 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C18 BGI A2022 " pdb=" C17 BGI A2022 " pdb=" C19 BGI A2022 " pdb=" O31 BGI A2022 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C17 BGI B1222 " pdb=" C16 BGI B1222 " pdb=" C18 BGI B1222 " pdb=" O21 BGI B1222 " both_signs ideal model delta sigma weight residual False 2.52 2.69 -0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 1861 not shown) Planarity restraints: 2038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 0V9 A2002 " 0.019 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C18 0V9 A2002 " -0.048 2.00e-02 2.50e+03 pdb=" C19 0V9 A2002 " 0.048 2.00e-02 2.50e+03 pdb=" C20 0V9 A2002 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 0V9 A2001 " -0.019 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C18 0V9 A2001 " 0.047 2.00e-02 2.50e+03 pdb=" C19 0V9 A2001 " -0.047 2.00e-02 2.50e+03 pdb=" C20 0V9 A2001 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 409 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO A 410 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 410 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 410 " -0.036 5.00e-02 4.00e+02 ... (remaining 2035 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 190 2.67 - 3.23: 11713 3.23 - 3.78: 18911 3.78 - 4.34: 27520 4.34 - 4.90: 45326 Nonbonded interactions: 103660 Sorted by model distance: nonbonded pdb=" OG SER A1027 " pdb=" N TYR A1028 " model vdw 2.112 3.120 nonbonded pdb=" O GLN B 398 " pdb=" OG1 THR B 401 " model vdw 2.267 3.040 nonbonded pdb=" O GLU A 591 " pdb=" NH1 ARG A 594 " model vdw 2.271 3.120 nonbonded pdb=" O GLN A 398 " pdb=" OG1 THR A 401 " model vdw 2.271 3.040 nonbonded pdb=" NZ LYS A 655 " pdb=" OE1 GLN A 934 " model vdw 2.282 3.120 ... (remaining 103655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 378 through 1131 or resid 2003 through 2008 or resid 2010 \ through 2012 or resid 2014 through 2019 or resid 2022)) selection = (chain 'B' and (resid 378 through 1131 or resid 1203 through 1208 or resid 1210 \ through 1212 or resid 1214 through 1219 or resid 1222)) } 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.250 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.283 12696 Z= 0.594 Angle : 0.819 8.130 16992 Z= 0.490 Chirality : 0.045 0.403 1864 Planarity : 0.005 0.067 2038 Dihedral : 15.457 123.518 4880 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.27 % Favored : 94.52 % Rotamer: Outliers : 0.61 % Allowed : 0.30 % Favored : 99.09 % 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: -1.32 (0.21), residues: 1442 helix: 0.18 (0.19), residues: 778 sheet: -3.16 (0.36), residues: 144 loop : -1.68 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B1047 HIS 0.003 0.001 HIS A 965 PHE 0.020 0.002 PHE B 813 TYR 0.014 0.002 TYR A 945 ARG 0.005 0.001 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.505 Fit side-chains TARDY: cannot create tardy model for: "ARG B1131 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A1131 " (corrupted residue). Skipping it. REVERT: B 934 GLN cc_start: 0.8035 (mt0) cc_final: 0.7592 (mt0) REVERT: B 1029 ASP cc_start: 0.7441 (m-30) cc_final: 0.7229 (m-30) REVERT: B 1124 PHE cc_start: 0.7312 (t80) cc_final: 0.6959 (t80) REVERT: A 594 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7847 (mmt-90) REVERT: A 1124 PHE cc_start: 0.7310 (t80) cc_final: 0.6949 (t80) outliers start: 8 outliers final: 2 residues processed: 178 average time/residue: 1.3276 time to fit residues: 256.6499 Evaluate side-chains 131 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1131 ARG Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 559 ASN B 574 GLN B 658 ASN B 689 GLN A 559 ASN A 574 GLN A 689 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12696 Z= 0.222 Angle : 0.544 5.945 16992 Z= 0.286 Chirality : 0.041 0.152 1864 Planarity : 0.005 0.048 2038 Dihedral : 11.054 112.646 2102 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.14 % Allowed : 8.50 % Favored : 90.36 % 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: -0.58 (0.21), residues: 1442 helix: 0.77 (0.19), residues: 808 sheet: -2.47 (0.38), residues: 144 loop : -1.59 (0.23), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1047 HIS 0.004 0.001 HIS B 540 PHE 0.019 0.002 PHE A 864 TYR 0.014 0.001 TYR B 945 ARG 0.009 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.366 Fit side-chains TARDY: cannot create tardy model for: "ARG B1131 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A1131 " (corrupted residue). Skipping it. REVERT: B 934 GLN cc_start: 0.8053 (mt0) cc_final: 0.7557 (mt0) REVERT: B 1112 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7488 (mtt180) REVERT: B 1124 PHE cc_start: 0.7296 (t80) cc_final: 0.6960 (t80) REVERT: A 478 LYS cc_start: 0.8333 (mmtp) cc_final: 0.8117 (mmmm) REVERT: A 594 ARG cc_start: 0.8091 (mmt-90) cc_final: 0.7878 (mmt-90) REVERT: A 934 GLN cc_start: 0.8136 (mt0) cc_final: 0.7581 (mt0) REVERT: A 1112 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7454 (mtt180) REVERT: A 1124 PHE cc_start: 0.7293 (t80) cc_final: 0.6957 (t80) outliers start: 15 outliers final: 3 residues processed: 150 average time/residue: 1.2455 time to fit residues: 204.9422 Evaluate side-chains 128 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1112 ARG Chi-restraints excluded: chain B residue 1131 ARG Chi-restraints excluded: chain A residue 1112 ARG Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 131 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 129 optimal weight: 0.0050 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 472 ASN B 559 ASN B 574 GLN B 689 GLN A 472 ASN A 559 ASN A 574 GLN A 689 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12696 Z= 0.355 Angle : 0.566 5.917 16992 Z= 0.294 Chirality : 0.043 0.157 1864 Planarity : 0.004 0.044 2038 Dihedral : 10.503 116.122 2102 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.12 % Allowed : 10.17 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.21), residues: 1442 helix: 0.96 (0.18), residues: 808 sheet: -2.29 (0.40), residues: 132 loop : -1.52 (0.23), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1047 HIS 0.006 0.002 HIS B 540 PHE 0.022 0.002 PHE B 864 TYR 0.011 0.002 TYR B 455 ARG 0.003 0.001 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.342 Fit side-chains TARDY: cannot create tardy model for: "ARG B1131 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A1131 " (corrupted residue). Skipping it. REVERT: B 934 GLN cc_start: 0.8038 (mt0) cc_final: 0.7510 (mt0) REVERT: B 1124 PHE cc_start: 0.7351 (t80) cc_final: 0.7005 (t80) REVERT: A 521 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7306 (m-30) REVERT: A 992 MET cc_start: 0.5925 (ptm) cc_final: 0.5083 (mpp) REVERT: A 1124 PHE cc_start: 0.7346 (t80) cc_final: 0.7000 (t80) outliers start: 28 outliers final: 11 residues processed: 139 average time/residue: 1.2524 time to fit residues: 190.9257 Evaluate side-chains 127 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1131 ARG Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 GLN B 689 GLN A 574 GLN A 658 ASN A 689 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12696 Z= 0.256 Angle : 0.500 5.795 16992 Z= 0.263 Chirality : 0.041 0.155 1864 Planarity : 0.004 0.041 2038 Dihedral : 9.984 114.278 2102 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.05 % Allowed : 11.91 % Favored : 86.04 % 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 (0.21), residues: 1442 helix: 1.24 (0.18), residues: 806 sheet: -1.95 (0.41), residues: 132 loop : -1.43 (0.23), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B1047 HIS 0.004 0.001 HIS B 540 PHE 0.019 0.002 PHE B 864 TYR 0.011 0.001 TYR B 455 ARG 0.005 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.515 Fit side-chains TARDY: cannot create tardy model for: "ARG B1131 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A1131 " (corrupted residue). Skipping it. REVERT: B 748 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: B 934 GLN cc_start: 0.8056 (mt0) cc_final: 0.7518 (mt0) REVERT: B 1124 PHE cc_start: 0.7371 (t80) cc_final: 0.7013 (t80) REVERT: A 689 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7803 (tm-30) REVERT: A 992 MET cc_start: 0.5692 (ptm) cc_final: 0.5041 (mpp) REVERT: A 1124 PHE cc_start: 0.7372 (t80) cc_final: 0.7016 (t80) outliers start: 27 outliers final: 12 residues processed: 144 average time/residue: 1.2090 time to fit residues: 191.2678 Evaluate side-chains 131 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1131 ARG Chi-restraints excluded: chain A residue 548 ASN Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 GLN B 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12696 Z= 0.152 Angle : 0.456 6.817 16992 Z= 0.240 Chirality : 0.039 0.152 1864 Planarity : 0.004 0.040 2038 Dihedral : 9.409 105.429 2102 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.44 % Allowed : 12.82 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.38 (0.22), residues: 1442 helix: 1.50 (0.19), residues: 806 sheet: -1.49 (0.41), residues: 144 loop : -1.28 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1047 HIS 0.002 0.001 HIS A 965 PHE 0.017 0.001 PHE B 864 TYR 0.011 0.001 TYR B 455 ARG 0.006 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.347 Fit side-chains TARDY: cannot create tardy model for: "ARG B1131 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARG A1131 " (corrupted residue). Skipping it. REVERT: B 934 GLN cc_start: 0.8078 (mt0) cc_final: 0.7501 (mt0) REVERT: B 1112 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7487 (mtt180) REVERT: B 1124 PHE cc_start: 0.7375 (t80) cc_final: 0.7018 (t80) REVERT: A 457 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: A 992 MET cc_start: 0.5728 (ptm) cc_final: 0.5087 (mpp) REVERT: A 1112 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7454 (mtt180) REVERT: A 1124 PHE cc_start: 0.7361 (t80) cc_final: 0.7005 (t80) outliers start: 19 outliers final: 9 residues processed: 138 average time/residue: 1.3019 time to fit residues: 196.6050 Evaluate side-chains 131 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 454 MET Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1112 ARG Chi-restraints excluded: chain B residue 1131 ARG Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1112 ARG Chi-restraints excluded: chain A residue 1131 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 574 GLN B 689 GLN A 574 GLN A 689 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 12696 Z= 0.403 Angle : 0.568 6.024 16992 Z= 0.293 Chirality : 0.044 0.157 1864 Planarity : 0.004 0.052 2038 Dihedral : 10.315 109.918 2102 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.82 % Allowed : 13.51 % Favored : 84.67 % 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: 0.25 (0.22), residues: 1442 helix: 1.29 (0.18), residues: 808 sheet: -1.37 (0.41), residues: 144 loop : -1.21 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B1047 HIS 0.007 0.002 HIS B 540 PHE 0.024 0.002 PHE B 864 TYR 0.016 0.002 TYR B 455 ARG 0.005 0.001 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.457 Fit side-chains revert: symmetry clash REVERT: B 748 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: B 934 GLN cc_start: 0.8124 (mt0) cc_final: 0.7538 (mt0) REVERT: B 992 MET cc_start: 0.6102 (ptm) cc_final: 0.5785 (ptm) REVERT: B 1124 PHE cc_start: 0.7392 (t80) cc_final: 0.7008 (t80) REVERT: A 457 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: A 689 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: A 1124 PHE cc_start: 0.7392 (t80) cc_final: 0.7010 (t80) outliers start: 24 outliers final: 12 residues processed: 135 average time/residue: 1.3056 time to fit residues: 192.2374 Evaluate side-chains 132 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 689 GLN A 574 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12696 Z= 0.233 Angle : 0.486 5.762 16992 Z= 0.257 Chirality : 0.040 0.155 1864 Planarity : 0.004 0.042 2038 Dihedral : 9.953 107.454 2094 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.59 % Allowed : 14.19 % Favored : 84.22 % 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 (0.22), residues: 1442 helix: 1.42 (0.18), residues: 810 sheet: -1.29 (0.41), residues: 146 loop : -1.11 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1047 HIS 0.004 0.001 HIS A 540 PHE 0.020 0.002 PHE B 864 TYR 0.010 0.001 TYR B 455 ARG 0.005 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: B 457 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: B 934 GLN cc_start: 0.8130 (mt0) cc_final: 0.7563 (mt0) REVERT: B 1124 PHE cc_start: 0.7393 (t80) cc_final: 0.7009 (t80) REVERT: A 457 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: A 1124 PHE cc_start: 0.7394 (t80) cc_final: 0.7024 (t80) outliers start: 21 outliers final: 12 residues processed: 137 average time/residue: 1.2779 time to fit residues: 191.0683 Evaluate side-chains 134 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 126 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 689 GLN A 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12696 Z= 0.157 Angle : 0.452 9.970 16992 Z= 0.237 Chirality : 0.039 0.153 1864 Planarity : 0.004 0.041 2038 Dihedral : 9.370 100.056 2094 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.67 % Allowed : 14.26 % Favored : 84.07 % 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: 0.74 (0.22), residues: 1442 helix: 1.70 (0.18), residues: 806 sheet: -1.13 (0.42), residues: 146 loop : -1.01 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1047 HIS 0.003 0.001 HIS B 828 PHE 0.020 0.001 PHE A 775 TYR 0.011 0.001 TYR A1067 ARG 0.005 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: B 457 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7211 (mp0) REVERT: B 594 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7777 (mmm-85) REVERT: B 934 GLN cc_start: 0.8136 (mt0) cc_final: 0.7556 (mt0) REVERT: B 992 MET cc_start: 0.5988 (ptm) cc_final: 0.5250 (mpp) REVERT: B 1112 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7466 (mtt180) REVERT: B 1124 PHE cc_start: 0.7384 (t80) cc_final: 0.7022 (t80) REVERT: A 457 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: A 1124 PHE cc_start: 0.7399 (t80) cc_final: 0.7037 (t80) outliers start: 22 outliers final: 9 residues processed: 141 average time/residue: 1.3087 time to fit residues: 201.1817 Evaluate side-chains 132 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1112 ARG Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1090 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 0.0060 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 689 GLN A 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12696 Z= 0.148 Angle : 0.453 10.618 16992 Z= 0.235 Chirality : 0.039 0.154 1864 Planarity : 0.004 0.041 2038 Dihedral : 8.990 94.772 2094 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.29 % Allowed : 14.34 % Favored : 84.37 % 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: 0.96 (0.22), residues: 1442 helix: 1.88 (0.18), residues: 800 sheet: -0.93 (0.43), residues: 146 loop : -0.92 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1047 HIS 0.002 0.001 HIS A 540 PHE 0.019 0.001 PHE B 775 TYR 0.012 0.001 TYR A1067 ARG 0.006 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: B 457 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: B 934 GLN cc_start: 0.8137 (mt0) cc_final: 0.7543 (mt0) REVERT: B 992 MET cc_start: 0.5936 (ptm) cc_final: 0.5201 (mpp) REVERT: B 1010 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7310 (pttt) REVERT: B 1124 PHE cc_start: 0.7384 (t80) cc_final: 0.7023 (t80) REVERT: A 457 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: A 748 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 1013 ASN cc_start: 0.8115 (t0) cc_final: 0.7794 (m110) REVERT: A 1124 PHE cc_start: 0.7402 (t80) cc_final: 0.7042 (t80) outliers start: 17 outliers final: 7 residues processed: 132 average time/residue: 1.3562 time to fit residues: 195.5450 Evaluate side-chains 127 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1090 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 689 GLN A 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12696 Z= 0.248 Angle : 0.505 8.500 16992 Z= 0.261 Chirality : 0.040 0.153 1864 Planarity : 0.004 0.040 2038 Dihedral : 9.466 103.812 2094 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.21 % Allowed : 14.42 % Favored : 84.37 % 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: 0.87 (0.22), residues: 1442 helix: 1.75 (0.18), residues: 806 sheet: -0.85 (0.43), residues: 146 loop : -0.93 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1047 HIS 0.005 0.001 HIS B 540 PHE 0.021 0.002 PHE B 864 TYR 0.010 0.001 TYR A1067 ARG 0.003 0.000 ARG B 508 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: B 457 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: B 934 GLN cc_start: 0.8104 (mt0) cc_final: 0.7506 (mt0) REVERT: B 992 MET cc_start: 0.5931 (ptm) cc_final: 0.5191 (mpp) REVERT: B 1010 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7312 (pttt) REVERT: B 1124 PHE cc_start: 0.7384 (t80) cc_final: 0.7010 (t80) REVERT: A 457 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: A 748 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 1013 ASN cc_start: 0.8088 (t0) cc_final: 0.7785 (m110) REVERT: A 1124 PHE cc_start: 0.7403 (t80) cc_final: 0.7036 (t80) outliers start: 16 outliers final: 10 residues processed: 132 average time/residue: 1.3338 time to fit residues: 192.1644 Evaluate side-chains 130 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 GLU Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1090 MET Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 689 GLN A 689 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.142081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103190 restraints weight = 13903.887| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.73 r_work: 0.2880 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12696 Z= 0.163 Angle : 0.460 8.910 16992 Z= 0.238 Chirality : 0.039 0.153 1864 Planarity : 0.004 0.041 2038 Dihedral : 9.094 99.711 2094 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.44 % Allowed : 14.26 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.22), residues: 1442 helix: 1.91 (0.18), residues: 800 sheet: -0.70 (0.44), residues: 146 loop : -0.85 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1047 HIS 0.003 0.001 HIS A 540 PHE 0.020 0.001 PHE A 775 TYR 0.011 0.001 TYR A1067 ARG 0.003 0.000 ARG B 620 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4084.06 seconds wall clock time: 74 minutes 39.08 seconds (4479.08 seconds total)