Starting phenix.real_space_refine on Thu Feb 15 14:11:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/02_2024/7xs6_33422_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/02_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_33422/02_2024/7xs6_33422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/02_2024/7xs6_33422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/02_2024/7xs6_33422_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xs6_33422/02_2024/7xs6_33422_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= 0.000 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 Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 573": "OE1" <-> "OE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B ASP 661": "OD1" <-> "OD2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 862": "OE1" <-> "OE2" Residue "B PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 909": "OE1" <-> "OE2" Residue "B TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 602": "OD1" <-> "OD2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 909": "OE1" <-> "OE2" Residue "A TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1119": "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: 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: 7.19, per 1000 atoms: 0.58 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 - 3.50 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: 6.36 Conformation dependent library (CDL) restraints added in 2.4 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... running ksdssp... Secondary structure from input PDB file: 60 helices and 10 sheets defined 51.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.81 Creating SS restraints... Processing helix chain 'B' and resid 393 through 402 removed outlier: 3.504A pdb=" N THR B 402 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 459 through 478 Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 507 through 515 Processing helix chain 'B' and resid 579 through 586 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 619 removed outlier: 3.683A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 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 645 through 660 Processing helix chain 'B' and resid 662 through 668 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 686 No H-bonds generated for 'chain 'B' and resid 683 through 686' Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 707 through 710 No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 718 through 725 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 750 through 773 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 777 No H-bonds generated for 'chain 'B' and resid 775 through 777' Processing helix chain 'B' and resid 785 through 806 removed outlier: 3.507A pdb=" N PHE B 796 " --> pdb=" O THR B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 827 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 829 through 854 removed outlier: 3.737A pdb=" N ASN B 832 " --> pdb=" O SER B 829 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 833 " --> pdb=" O ALA B 830 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 834 " --> pdb=" O PHE B 831 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE B 837 " --> pdb=" O LEU B 834 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B 838 " --> pdb=" O SER B 835 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 841 " --> pdb=" O PHE B 838 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER B 848 " --> pdb=" O CYS B 845 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 852 " --> pdb=" O THR B 849 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 853 " --> pdb=" O PHE B 850 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 854 " --> pdb=" O ILE B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 894 Processing helix chain 'B' and resid 922 through 931 Processing helix chain 'B' and resid 937 through 940 No H-bonds generated for 'chain 'B' and resid 937 through 940' Processing helix chain 'B' and resid 943 through 953 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 962 Processing helix chain 'B' and resid 998 through 1011 Processing helix chain 'B' and resid 1029 through 1058 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 1064 through 1074 Processing helix chain 'B' and resid 1092 through 1129 removed outlier: 3.795A pdb=" N VAL B1105 " --> pdb=" O ILE B1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 402 removed outlier: 3.500A pdb=" N THR A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 459 through 478 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 507 through 515 Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 611 through 619 removed outlier: 3.758A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 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 645 through 657 Processing helix chain 'A' and resid 662 through 668 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 686 No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 707 through 710 No H-bonds generated for 'chain 'A' and resid 707 through 710' Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 719 through 725 removed outlier: 3.697A pdb=" N VAL A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 773 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 777 No H-bonds generated for 'chain 'A' and resid 775 through 777' Processing helix chain 'A' and resid 785 through 806 Processing helix chain 'A' and resid 808 through 827 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 829 through 854 removed outlier: 3.734A pdb=" N ASN A 832 " --> pdb=" O SER A 829 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 833 " --> pdb=" O ALA A 830 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 834 " --> pdb=" O PHE A 831 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 838 " --> pdb=" O SER A 835 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 841 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 847 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 848 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 852 " --> pdb=" O THR A 849 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 853 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 854 " --> pdb=" O ILE A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 894 Processing helix chain 'A' and resid 922 through 931 Processing helix chain 'A' and resid 937 through 940 No H-bonds generated for 'chain 'A' and resid 937 through 940' Processing helix chain 'A' and resid 943 through 953 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 962 Processing helix chain 'A' and resid 998 through 1011 removed outlier: 3.524A pdb=" N VAL A1011 " --> pdb=" O LYS A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1058 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 1064 through 1074 Processing helix chain 'A' and resid 1092 through 1129 removed outlier: 3.786A pdb=" N VAL A1105 " --> pdb=" O ILE A1101 " (cutoff:3.500A) Processing sheet with id= A, 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) Processing sheet with id= B, first strand: chain 'B' and resid 493 through 499 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) Processing sheet with id= C, first strand: chain 'B' and resid 540 through 542 Processing sheet with id= D, first strand: chain 'B' and resid 545 through 549 removed outlier: 3.550A pdb=" N ASN B 545 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 627 through 633 removed outlier: 6.696A pdb=" N LYS B 735 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLU B 630 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N CYS B 737 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 9.855A pdb=" N ARG B 632 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 13.906A pdb=" N SER B 739 " --> pdb=" O ARG B 632 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, 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) Processing sheet with id= G, first strand: chain 'A' and resid 493 through 499 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) Processing sheet with id= H, first strand: chain 'A' and resid 540 through 542 Processing sheet with id= I, first strand: chain 'A' and resid 545 through 549 removed outlier: 3.554A pdb=" N ASN A 545 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.659A pdb=" N LYS A 735 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N GLU A 630 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N CYS A 737 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 9.810A pdb=" N ARG A 632 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 13.877A pdb=" N SER A 739 " --> pdb=" O ARG A 632 " (cutoff:3.500A) No H-bonds generated for sheet with id= J 513 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 6.69 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: 97.83 - 105.08: 171 105.08 - 112.32: 6046 112.32 - 119.56: 4670 119.56 - 126.80: 5953 126.80 - 134.04: 152 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: 191 2.67 - 3.23: 11820 3.23 - 3.78: 19000 3.78 - 4.34: 27747 4.34 - 4.90: 45346 Nonbonded interactions: 104104 Sorted by model distance: nonbonded pdb=" OG SER A1027 " pdb=" N TYR A1028 " model vdw 2.112 2.520 nonbonded pdb=" O GLN B 398 " pdb=" OG1 THR B 401 " model vdw 2.267 2.440 nonbonded pdb=" O GLU A 591 " pdb=" NH1 ARG A 594 " model vdw 2.271 2.520 nonbonded pdb=" O GLN A 398 " pdb=" OG1 THR A 401 " model vdw 2.271 2.440 nonbonded pdb=" NZ LYS A 655 " pdb=" OE1 GLN A 934 " model vdw 2.282 2.520 ... (remaining 104099 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 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: 0.880 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: 3.740 Check model and map are aligned: 0.200 Set scattering table: 0.100 Process input model: 37.910 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.570 ------------------------------------------------------------------------------- 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= 0.511 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 fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 1.354 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: 1.2893 time to fit residues: 249.8680 Evaluate side-chains 131 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 129 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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: 0.8980 chunk 109 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 30.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 689 GLN B1002 GLN A 559 ASN A 574 GLN A 689 GLN A1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12696 Z= 0.234 Angle : 0.531 5.868 16992 Z= 0.277 Chirality : 0.041 0.154 1864 Planarity : 0.004 0.048 2038 Dihedral : 11.174 113.501 2102 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.44 % Allowed : 8.19 % 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: -0.87 (0.21), residues: 1442 helix: 0.50 (0.19), residues: 786 sheet: -2.62 (0.37), residues: 144 loop : -1.55 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1047 HIS 0.003 0.001 HIS A 459 PHE 0.017 0.001 PHE B 864 TYR 0.013 0.002 TYR A 455 ARG 0.004 0.000 ARG B 508 *********************** 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 152 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.243 Fit side-chains revert: symmetry clash 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 478 LYS cc_start: 0.8309 (mmtp) cc_final: 0.8107 (mmmm) REVERT: B 934 GLN cc_start: 0.8014 (mt0) cc_final: 0.7573 (mt0) REVERT: B 1124 PHE cc_start: 0.7293 (t80) cc_final: 0.6957 (t80) REVERT: A 416 MET cc_start: 0.8366 (tmm) cc_final: 0.8155 (tmm) REVERT: A 478 LYS cc_start: 0.8313 (mmtp) cc_final: 0.8108 (mmmm) REVERT: A 594 ARG cc_start: 0.8166 (mmt-90) cc_final: 0.7858 (mmt-90) REVERT: A 1112 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7453 (mtt180) REVERT: A 1124 PHE cc_start: 0.7294 (t80) cc_final: 0.6959 (t80) outliers start: 19 outliers final: 4 residues processed: 141 average time/residue: 1.1265 time to fit residues: 175.0762 Evaluate side-chains 122 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.372 ------------------------------------------------------------------------------- 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: 0.7980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 B1002 GLN A 472 ASN A 559 ASN A 574 GLN A 689 GLN A1002 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12696 Z= 0.245 Angle : 0.491 5.773 16992 Z= 0.257 Chirality : 0.040 0.155 1864 Planarity : 0.004 0.040 2038 Dihedral : 9.961 113.511 2102 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 9.48 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1442 helix: 0.74 (0.19), residues: 786 sheet: -2.23 (0.38), residues: 144 loop : -1.45 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1047 HIS 0.004 0.001 HIS B 540 PHE 0.018 0.002 PHE B 864 TYR 0.011 0.001 TYR B 455 ARG 0.003 0.000 ARG B 508 *********************** 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 151 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.383 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B1131 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG A1131 " (corrupted residue). Skipping it. REVERT: B 521 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: B 594 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7914 (mmt-90) REVERT: B 748 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: B 934 GLN cc_start: 0.7948 (mt0) cc_final: 0.7485 (mt0) REVERT: B 1124 PHE cc_start: 0.7346 (t80) cc_final: 0.7008 (t80) REVERT: A 416 MET cc_start: 0.8438 (tmm) cc_final: 0.8169 (tmm) REVERT: A 521 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: A 594 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7885 (mmt-90) REVERT: A 992 MET cc_start: 0.5899 (ptm) cc_final: 0.5095 (mpp) REVERT: A 1124 PHE cc_start: 0.7323 (t80) cc_final: 0.6985 (t80) outliers start: 27 outliers final: 10 residues processed: 143 average time/residue: 1.1071 time to fit residues: 174.7123 Evaluate side-chains 132 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 548 ASN Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1112 ARG Chi-restraints excluded: chain B residue 1131 ARG Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1010 LYS Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1112 ARG 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: 4.9990 chunk 98 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 62 optimal weight: 8.9990 chunk 87 optimal weight: 0.2980 chunk 131 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 68 optimal weight: 0.0060 chunk 124 optimal weight: 9.9990 chunk 37 optimal weight: 0.0970 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 B1002 GLN ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN A 574 GLN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 689 GLN A1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12696 Z= 0.117 Angle : 0.415 5.537 16992 Z= 0.220 Chirality : 0.038 0.152 1864 Planarity : 0.003 0.040 2038 Dihedral : 8.870 102.875 2102 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.97 % Allowed : 10.93 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1442 helix: 1.17 (0.19), residues: 782 sheet: -1.74 (0.41), residues: 144 loop : -1.32 (0.23), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1047 HIS 0.001 0.000 HIS B 459 PHE 0.015 0.001 PHE B 775 TYR 0.011 0.001 TYR A1067 ARG 0.004 0.000 ARG B1040 *********************** 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 150 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.521 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B1131 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG A1131 " (corrupted residue). Skipping it. REVERT: B 594 ARG cc_start: 0.8187 (mmt-90) cc_final: 0.7786 (mmt-90) REVERT: B 716 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: B 934 GLN cc_start: 0.7998 (mt0) cc_final: 0.7471 (mt0) REVERT: B 992 MET cc_start: 0.5898 (ptt) cc_final: 0.5172 (mpp) REVERT: B 1002 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7228 (mm-40) REVERT: B 1124 PHE cc_start: 0.7338 (t80) cc_final: 0.6998 (t80) REVERT: A 416 MET cc_start: 0.8346 (tmm) cc_final: 0.8131 (tmm) REVERT: A 594 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7880 (mmt-90) REVERT: A 992 MET cc_start: 0.5679 (ptm) cc_final: 0.5043 (mpp) REVERT: A 1124 PHE cc_start: 0.7338 (t80) cc_final: 0.7000 (t80) outliers start: 26 outliers final: 7 residues processed: 142 average time/residue: 1.0981 time to fit residues: 172.3577 Evaluate side-chains 127 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 1002 GLN 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 928 SER Chi-restraints excluded: chain A residue 1112 ARG 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: 1.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 689 GLN B1002 GLN A 559 ASN A 574 GLN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 689 GLN A1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12696 Z= 0.207 Angle : 0.453 6.569 16992 Z= 0.236 Chirality : 0.039 0.156 1864 Planarity : 0.004 0.038 2038 Dihedral : 8.905 100.817 2102 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.44 % Allowed : 12.22 % Favored : 86.34 % 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: 0.03 (0.22), residues: 1442 helix: 1.14 (0.19), residues: 786 sheet: -1.55 (0.41), residues: 144 loop : -1.21 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1047 HIS 0.004 0.001 HIS B 540 PHE 0.017 0.001 PHE B1052 TYR 0.009 0.001 TYR B 959 ARG 0.002 0.000 ARG B1040 *********************** 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 138 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 559 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.8169 (p0) REVERT: B 594 ARG cc_start: 0.8173 (mmt-90) cc_final: 0.7855 (mmt-90) REVERT: B 992 MET cc_start: 0.5948 (ptt) cc_final: 0.5157 (mpp) REVERT: B 1124 PHE cc_start: 0.7352 (t80) cc_final: 0.7003 (t80) REVERT: A 521 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: A 559 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8175 (p0) REVERT: A 594 ARG cc_start: 0.8145 (mmt-90) cc_final: 0.7923 (mmt-90) REVERT: A 689 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: A 992 MET cc_start: 0.5743 (ptm) cc_final: 0.5093 (mpp) REVERT: A 1124 PHE cc_start: 0.7350 (t80) cc_final: 0.6995 (t80) outliers start: 19 outliers final: 7 residues processed: 132 average time/residue: 1.1517 time to fit residues: 167.8513 Evaluate side-chains 126 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 928 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 521 ASP Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 689 GLN Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1112 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12696 Z= 0.224 Angle : 0.465 7.504 16992 Z= 0.242 Chirality : 0.039 0.153 1864 Planarity : 0.004 0.038 2038 Dihedral : 8.843 101.838 2094 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.67 % Allowed : 13.13 % Favored : 85.20 % 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: 0.06 (0.22), residues: 1442 helix: 1.13 (0.19), residues: 786 sheet: -1.43 (0.42), residues: 144 loop : -1.16 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1047 HIS 0.004 0.001 HIS B 540 PHE 0.017 0.001 PHE B1052 TYR 0.009 0.001 TYR B 959 ARG 0.002 0.000 ARG B1040 *********************** 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 142 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 458 ASP cc_start: 0.7713 (t0) cc_final: 0.7492 (t70) REVERT: B 521 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: B 594 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7957 (mmt-90) REVERT: B 716 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: B 748 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: B 832 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7851 (t0) REVERT: B 992 MET cc_start: 0.5954 (ptt) cc_final: 0.5145 (mpp) REVERT: B 1124 PHE cc_start: 0.7377 (t80) cc_final: 0.7024 (t80) REVERT: A 521 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7235 (m-30) REVERT: A 594 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7921 (mmt-90) REVERT: A 832 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7834 (t0) REVERT: A 1124 PHE cc_start: 0.7357 (t80) cc_final: 0.7009 (t80) outliers start: 22 outliers final: 11 residues processed: 133 average time/residue: 1.2888 time to fit residues: 187.5583 Evaluate side-chains 134 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 928 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 B residue 1112 ARG Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1112 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 B1002 GLN A 574 GLN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12696 Z= 0.156 Angle : 0.435 7.952 16992 Z= 0.226 Chirality : 0.038 0.151 1864 Planarity : 0.003 0.038 2038 Dihedral : 8.669 99.453 2094 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.52 % Allowed : 13.88 % Favored : 84.60 % 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: 0.24 (0.22), residues: 1442 helix: 1.27 (0.19), residues: 784 sheet: -1.31 (0.42), residues: 146 loop : -1.08 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1047 HIS 0.002 0.001 HIS B 540 PHE 0.016 0.001 PHE B 775 TYR 0.009 0.001 TYR A1067 ARG 0.003 0.000 ARG B1040 *********************** 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 135 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 521 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: B 594 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7883 (mmt-90) REVERT: B 716 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: B 832 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7720 (t0) REVERT: B 992 MET cc_start: 0.5961 (ptt) cc_final: 0.5143 (mpp) REVERT: B 1124 PHE cc_start: 0.7378 (t80) cc_final: 0.7026 (t80) REVERT: A 521 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: A 594 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7905 (mmt-90) REVERT: A 832 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7775 (t0) REVERT: A 1124 PHE cc_start: 0.7357 (t80) cc_final: 0.7008 (t80) outliers start: 20 outliers final: 4 residues processed: 127 average time/residue: 1.1393 time to fit residues: 158.8369 Evaluate side-chains 124 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 521 ASP Chi-restraints excluded: chain B residue 716 GLU Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 1010 LYS Chi-restraints excluded: chain B residue 1112 ARG Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1112 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 88 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 126 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 B1002 GLN A 574 GLN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12696 Z= 0.121 Angle : 0.412 6.890 16992 Z= 0.214 Chirality : 0.038 0.149 1864 Planarity : 0.003 0.039 2038 Dihedral : 8.204 91.156 2094 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.99 % Allowed : 14.72 % 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: 0.47 (0.22), residues: 1442 helix: 1.46 (0.19), residues: 780 sheet: -1.05 (0.43), residues: 146 loop : -1.02 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1047 HIS 0.001 0.000 HIS B 540 PHE 0.016 0.001 PHE A 775 TYR 0.010 0.001 TYR A1067 ARG 0.003 0.000 ARG A1040 *********************** 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 137 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 124 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 594 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.7816 (mmt-90) REVERT: B 992 MET cc_start: 0.5860 (ptt) cc_final: 0.5186 (mpp) REVERT: B 1124 PHE cc_start: 0.7380 (t80) cc_final: 0.7027 (t80) REVERT: A 594 ARG cc_start: 0.8121 (mmt-90) cc_final: 0.7826 (mmt-90) REVERT: A 1013 ASN cc_start: 0.8016 (t0) cc_final: 0.7683 (m110) REVERT: A 1124 PHE cc_start: 0.7361 (t80) cc_final: 0.7012 (t80) outliers start: 13 outliers final: 7 residues processed: 130 average time/residue: 1.2831 time to fit residues: 182.0464 Evaluate side-chains 124 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 775 PHE 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 543 MET Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1112 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN A 574 GLN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12696 Z= 0.199 Angle : 0.447 6.627 16992 Z= 0.232 Chirality : 0.039 0.150 1864 Planarity : 0.003 0.038 2038 Dihedral : 8.570 96.435 2094 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.37 % Allowed : 14.64 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1442 helix: 1.36 (0.19), residues: 784 sheet: -0.93 (0.43), residues: 146 loop : -0.95 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1047 HIS 0.004 0.001 HIS A 540 PHE 0.016 0.001 PHE B 864 TYR 0.008 0.001 TYR B 959 ARG 0.002 0.000 ARG A1040 *********************** 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 134 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 508 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8033 (mtm180) REVERT: B 594 ARG cc_start: 0.8160 (mmt-90) cc_final: 0.7845 (mmt-90) REVERT: B 748 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: B 992 MET cc_start: 0.5899 (ptt) cc_final: 0.5195 (mpp) REVERT: B 1124 PHE cc_start: 0.7383 (t80) cc_final: 0.7019 (t80) REVERT: A 559 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8268 (p0) REVERT: A 594 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7861 (mmt-90) REVERT: A 1013 ASN cc_start: 0.8028 (t0) cc_final: 0.7704 (m110) REVERT: A 1124 PHE cc_start: 0.7359 (t80) cc_final: 0.7008 (t80) outliers start: 18 outliers final: 9 residues processed: 125 average time/residue: 1.2309 time to fit residues: 168.5202 Evaluate side-chains 127 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 748 GLU 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 B residue 1112 ARG Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 928 SER Chi-restraints excluded: chain A residue 1090 MET Chi-restraints excluded: chain A residue 1112 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN B 574 GLN B 689 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN A 574 GLN A1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12696 Z= 0.310 Angle : 0.510 6.252 16992 Z= 0.264 Chirality : 0.041 0.152 1864 Planarity : 0.004 0.042 2038 Dihedral : 9.435 107.713 2094 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.14 % Allowed : 14.95 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1442 helix: 1.11 (0.19), residues: 790 sheet: -0.87 (0.43), residues: 144 loop : -0.99 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B1047 HIS 0.006 0.001 HIS A 540 PHE 0.021 0.002 PHE B1052 TYR 0.010 0.002 TYR B 696 ARG 0.002 0.000 ARG B 632 ********************** 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 136 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: B 458 ASP cc_start: 0.7810 (t0) cc_final: 0.7533 (t70) REVERT: B 508 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8073 (mtm180) REVERT: B 594 ARG cc_start: 0.8211 (mmt-90) cc_final: 0.8004 (mmt-90) REVERT: B 748 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 992 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5210 (mpp) REVERT: B 1124 PHE cc_start: 0.7389 (t80) cc_final: 0.7017 (t80) REVERT: A 594 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7929 (mmt-90) REVERT: A 1013 ASN cc_start: 0.8018 (t0) cc_final: 0.7763 (m110) REVERT: A 1124 PHE cc_start: 0.7365 (t80) cc_final: 0.6996 (t80) outliers start: 15 outliers final: 8 residues processed: 129 average time/residue: 1.2083 time to fit residues: 170.9682 Evaluate side-chains 130 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 ARG Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 992 MET 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 539 GLU Chi-restraints excluded: chain A residue 928 SER 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: 0.5980 chunk 34 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN B 574 GLN B 689 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN A 574 GLN ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.143133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104834 restraints weight = 13912.908| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.72 r_work: 0.2842 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12696 Z= 0.135 Angle : 0.425 6.558 16992 Z= 0.221 Chirality : 0.038 0.148 1864 Planarity : 0.003 0.040 2038 Dihedral : 8.764 98.843 2094 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.06 % Allowed : 14.95 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.51 (0.22), residues: 1442 helix: 1.39 (0.19), residues: 784 sheet: -0.82 (0.43), residues: 146 loop : -0.90 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1047 HIS 0.002 0.001 HIS B 540 PHE 0.018 0.001 PHE B 775 TYR 0.009 0.001 TYR A1067 ARG 0.002 0.000 ARG A1040 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.06 seconds wall clock time: 71 minutes 47.03 seconds (4307.03 seconds total)