Starting phenix.real_space_refine on Wed Mar 20 10:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtd_32779/03_2024/7wtd_32779_updated.pdb" } resolution = 3.9 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= 0.001 sd= 0.005 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 12 5.49 5 S 152 5.16 5 C 17157 2.51 5 N 4733 2.21 5 O 5083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 937": "OE1" <-> "OE2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 353": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ARG 496": "NH1" <-> "NH2" Residue "C GLU 1097": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D ARG 445": "NH1" <-> "NH2" Residue "D GLU 483": "OE1" <-> "OE2" Residue "D GLU 961": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27137 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "B" Number of atoms: 4625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4625 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 40, 'TRANS': 559} Chain: "C" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'CIS': 1, 'PTRANS': 65, 'TRANS': 1079} Chain: "D" Number of atoms: 8860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1145, 8860 Classifications: {'peptide': 1145} Link IDs: {'PTRANS': 65, 'TRANS': 1079} Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'ATP': 1, 'COA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'ATP': 1, 'COA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.92, per 1000 atoms: 0.51 Number of scatterers: 27137 At special positions: 0 Unit cell: (159.5, 152.9, 134.2, 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 152 16.00 P 12 15.00 O 5083 8.00 N 4733 7.00 C 17157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 752 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.02 Simple disulfide: pdb=" SG CYS C 752 " - pdb=" SG CYS C 786 " distance=2.03 Simple disulfide: pdb=" SG CYS D 752 " - pdb=" SG CYS D 786 " distance=2.02 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.90 Conformation dependent library (CDL) restraints added in 5.0 seconds 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6426 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 24 sheets defined 39.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.04 Creating SS restraints... Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 584 through 597 removed outlier: 3.758A pdb=" N LYS A 589 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE A 590 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Proline residue: A 592 - end of helix Processing helix chain 'A' and resid 609 through 616 removed outlier: 4.933A pdb=" N ASP A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A 614 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.766A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 668 Processing helix chain 'A' and resid 683 through 696 Processing helix chain 'A' and resid 720 through 733 Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 774 through 776 No H-bonds generated for 'chain 'A' and resid 774 through 776' Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 810 through 816 Processing helix chain 'A' and resid 828 through 843 removed outlier: 3.887A pdb=" N GLY A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 853 No H-bonds generated for 'chain 'A' and resid 850 through 853' Processing helix chain 'A' and resid 861 through 864 No H-bonds generated for 'chain 'A' and resid 861 through 864' Processing helix chain 'A' and resid 868 through 881 Processing helix chain 'A' and resid 886 through 900 removed outlier: 3.982A pdb=" N VAL A 890 " --> pdb=" O LYS A 886 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 896 " --> pdb=" O LYS A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'A' and resid 978 through 981 No H-bonds generated for 'chain 'A' and resid 978 through 981' Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1004 through 1012 Processing helix chain 'A' and resid 1014 through 1027 Processing helix chain 'A' and resid 1035 through 1039 Processing helix chain 'B' and resid 497 through 509 Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 550 through 559 Processing helix chain 'B' and resid 572 through 577 Processing helix chain 'B' and resid 584 through 587 No H-bonds generated for 'chain 'B' and resid 584 through 587' Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 623 through 628 Processing helix chain 'B' and resid 656 through 669 Processing helix chain 'B' and resid 683 through 696 Processing helix chain 'B' and resid 720 through 733 removed outlier: 3.533A pdb=" N MET B 724 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 762 removed outlier: 4.194A pdb=" N ARG B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 810 through 816 Processing helix chain 'B' and resid 829 through 845 removed outlier: 3.640A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR B 845 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 864 No H-bonds generated for 'chain 'B' and resid 861 through 864' Processing helix chain 'B' and resid 868 through 880 removed outlier: 3.838A pdb=" N ASN B 873 " --> pdb=" O GLY B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 900 removed outlier: 3.766A pdb=" N ALA B 893 " --> pdb=" O VAL B 890 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 895 " --> pdb=" O LYS B 892 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU B 896 " --> pdb=" O ALA B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 923 Processing helix chain 'B' and resid 928 through 933 Processing helix chain 'B' and resid 942 through 949 Processing helix chain 'B' and resid 961 through 968 Processing helix chain 'B' and resid 978 through 981 No H-bonds generated for 'chain 'B' and resid 978 through 981' Processing helix chain 'B' and resid 987 through 998 Processing helix chain 'B' and resid 1004 through 1012 Processing helix chain 'B' and resid 1014 through 1027 Processing helix chain 'B' and resid 1035 through 1039 Processing helix chain 'C' and resid 47 through 59 removed outlier: 3.523A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.548A pdb=" N ASN C 109 " --> pdb=" O VAL C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.759A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 302 Processing helix chain 'C' and resid 333 through 339 Processing helix chain 'C' and resid 344 through 353 Processing helix chain 'C' and resid 357 through 360 No H-bonds generated for 'chain 'C' and resid 357 through 360' Processing helix chain 'C' and resid 436 through 449 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 469 through 473 Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 498 through 510 Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 550 through 558 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 587 through 589 No H-bonds generated for 'chain 'C' and resid 587 through 589' Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 609 through 611 No H-bonds generated for 'chain 'C' and resid 609 through 611' Processing helix chain 'C' and resid 623 through 633 removed outlier: 4.550A pdb=" N GLU C 629 " --> pdb=" O ARG C 625 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 631 " --> pdb=" O LEU C 627 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU C 632 " --> pdb=" O GLN C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 669 Processing helix chain 'C' and resid 683 through 696 Processing helix chain 'C' and resid 720 through 733 Processing helix chain 'C' and resid 749 through 760 Processing helix chain 'C' and resid 779 through 789 Processing helix chain 'C' and resid 799 through 801 No H-bonds generated for 'chain 'C' and resid 799 through 801' Processing helix chain 'C' and resid 810 through 816 Processing helix chain 'C' and resid 830 through 845 removed outlier: 3.881A pdb=" N LEU C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N TYR C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 853 No H-bonds generated for 'chain 'C' and resid 850 through 853' Processing helix chain 'C' and resid 861 through 864 No H-bonds generated for 'chain 'C' and resid 861 through 864' Processing helix chain 'C' and resid 868 through 880 removed outlier: 4.349A pdb=" N THR C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN C 873 " --> pdb=" O GLY C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 892 Processing helix chain 'C' and resid 894 through 900 Processing helix chain 'C' and resid 909 through 924 Processing helix chain 'C' and resid 928 through 933 Processing helix chain 'C' and resid 942 through 949 Processing helix chain 'C' and resid 961 through 967 Processing helix chain 'C' and resid 978 through 981 No H-bonds generated for 'chain 'C' and resid 978 through 981' Processing helix chain 'C' and resid 988 through 997 removed outlier: 3.869A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1026 Proline residue: C1014 - end of helix Processing helix chain 'C' and resid 1035 through 1039 Processing helix chain 'D' and resid 47 through 59 removed outlier: 3.511A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 99 through 108 Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 143 through 149 Processing helix chain 'D' and resid 152 through 161 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'D' and resid 210 through 227 removed outlier: 3.797A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 302 Processing helix chain 'D' and resid 331 through 339 removed outlier: 4.057A pdb=" N THR D 334 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 357 through 360 Processing helix chain 'D' and resid 436 through 449 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 469 through 473 Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 496 through 509 Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 550 through 559 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 584 through 597 Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 609 through 617 removed outlier: 3.641A pdb=" N ASP D 613 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET D 616 " --> pdb=" O PHE D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 633 Processing helix chain 'D' and resid 656 through 669 Processing helix chain 'D' and resid 683 through 696 Processing helix chain 'D' and resid 720 through 733 Processing helix chain 'D' and resid 749 through 760 Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 810 through 815 Processing helix chain 'D' and resid 828 through 845 removed outlier: 3.995A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR D 845 " --> pdb=" O ALA D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 853 No H-bonds generated for 'chain 'D' and resid 850 through 853' Processing helix chain 'D' and resid 868 through 881 removed outlier: 3.605A pdb=" N THR D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN D 873 " --> pdb=" O GLY D 869 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 874 " --> pdb=" O GLN D 870 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA D 878 " --> pdb=" O LEU D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 900 removed outlier: 4.093A pdb=" N VAL D 895 " --> pdb=" O LYS D 891 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU D 896 " --> pdb=" O LYS D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 924 Processing helix chain 'D' and resid 928 through 933 Processing helix chain 'D' and resid 942 through 949 Processing helix chain 'D' and resid 961 through 968 Processing helix chain 'D' and resid 978 through 981 No H-bonds generated for 'chain 'D' and resid 978 through 981' Processing helix chain 'D' and resid 987 through 997 removed outlier: 4.068A pdb=" N GLU D 991 " --> pdb=" O LEU D 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS D 992 " --> pdb=" O GLN D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1004 through 1012 Processing helix chain 'D' and resid 1014 through 1027 Processing helix chain 'D' and resid 1035 through 1039 Processing sheet with id= A, first strand: chain 'A' and resid 564 through 567 Processing sheet with id= B, first strand: chain 'A' and resid 642 through 644 removed outlier: 8.120A pdb=" N LEU A 643 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG A 675 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 699 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N VAL A 676 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU A 701 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 737 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE A 704 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS A 739 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1047 through 1050 removed outlier: 3.611A pdb=" N VAL A1050 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A1058 " --> pdb=" O VAL A1050 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS A1061 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A1079 " --> pdb=" O LYS A1061 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A1063 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N PHE A1077 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N VAL A1065 " --> pdb=" O GLN A1075 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN A1075 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 564 through 567 removed outlier: 3.516A pdb=" N VAL B 796 " --> pdb=" O MET B 566 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 603 through 605 removed outlier: 7.050A pdb=" N VAL B 673 " --> pdb=" O MET B 641 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL B 699 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL B 676 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLU B 701 " --> pdb=" O VAL B 676 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE B 737 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE B 704 " --> pdb=" O ILE B 737 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 739 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N ILE B 740 " --> pdb=" O PRO B 767 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N HIS B 769 " --> pdb=" O ILE B 740 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASP B 742 " --> pdb=" O HIS B 769 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS B 771 " --> pdb=" O ASP B 742 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 3.581A pdb=" N VAL B1050 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B1058 " --> pdb=" O VAL B1050 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B1061 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B1079 " --> pdb=" O LYS B1061 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B1063 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 137 through 139 removed outlier: 6.519A pdb=" N ARG C 62 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL C 42 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N VAL C 64 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLU C 82 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR C 67 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR C 84 " --> pdb=" O TYR C 67 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 191 through 195 removed outlier: 3.771A pdb=" N GLU C 236 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 262 through 264 Processing sheet with id= J, first strand: chain 'C' and resid 249 through 251 Processing sheet with id= K, first strand: chain 'C' and resid 275 through 277 removed outlier: 3.677A pdb=" N VAL C 427 " --> pdb=" O VAL C 378 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 396 through 398 removed outlier: 4.078A pdb=" N ARG C 451 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 564 through 566 Processing sheet with id= N, first strand: chain 'C' and resid 603 through 605 No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 642 through 644 removed outlier: 7.956A pdb=" N LEU C 643 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG C 675 " --> pdb=" O LEU C 643 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL C 699 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL C 676 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU C 701 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE C 737 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ILE C 704 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N CYS C 739 " --> pdb=" O ILE C 704 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1085 through 1090 removed outlier: 3.538A pdb=" N VAL C1076 " --> pdb=" O ILE C1087 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLU C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA C1062 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C1053 " --> pdb=" O LYS C1056 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N LEU C1058 " --> pdb=" O GLU C1051 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLU C1051 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE C1060 " --> pdb=" O GLU C1049 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU C1049 " --> pdb=" O ILE C1060 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ALA C1062 " --> pdb=" O GLU C1047 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLU C1047 " --> pdb=" O ALA C1062 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 137 through 139 removed outlier: 3.640A pdb=" N ALA D 113 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG D 62 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL D 42 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL D 64 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU D 82 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR D 67 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR D 84 " --> pdb=" O TYR D 67 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 204 through 207 removed outlier: 3.510A pdb=" N ARG D 205 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 257 through 259 removed outlier: 3.843A pdb=" N GLU D 324 " --> pdb=" O GLU D 311 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 275 through 277 removed outlier: 3.657A pdb=" N VAL D 427 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 564 through 567 Processing sheet with id= V, first strand: chain 'D' and resid 768 through 771 removed outlier: 7.018A pdb=" N LEU D 738 " --> pdb=" O HIS D 769 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N HIS D 771 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE D 740 " --> pdb=" O HIS D 771 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 674 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.126A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 1047 through 1051 removed outlier: 6.512A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL D1065 " --> pdb=" O GLN D1075 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN D1075 " --> pdb=" O VAL D1065 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 1112 through 1114 removed outlier: 5.635A pdb=" N ALA D1114 " --> pdb=" O LEU D1173 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU D1173 " --> pdb=" O ALA D1114 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2586 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: 9.03 Time building geometry restraints manager: 12.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.68: 27479 1.68 - 2.20: 262 2.20 - 2.71: 0 2.71 - 3.23: 1 3.23 - 3.74: 3 Bond restraints: 27745 Sorted by residual: bond pdb=" AO6 COA C2001 " pdb=" AP2 COA C2001 " ideal model delta sigma weight residual 1.610 3.742 -2.132 2.00e-02 2.50e+03 1.14e+04 bond pdb=" AP1 COA D2001 " pdb="AO5* COA D2001 " ideal model delta sigma weight residual 1.610 3.585 -1.975 2.00e-02 2.50e+03 9.76e+03 bond pdb=" AP1 COA C2001 " pdb="AO5* COA C2001 " ideal model delta sigma weight residual 1.610 3.258 -1.648 2.00e-02 2.50e+03 6.79e+03 bond pdb=" AO6 COA D2001 " pdb=" AP2 COA D2001 " ideal model delta sigma weight residual 1.610 3.225 -1.615 2.00e-02 2.50e+03 6.52e+03 bond pdb=" PC9 COA C2001 " pdb=" PO9 COA C2001 " ideal model delta sigma weight residual 1.410 1.170 0.240 2.00e-02 2.50e+03 1.44e+02 ... (remaining 27740 not shown) Histogram of bond angle deviations from ideal: 40.50 - 65.25: 5 65.25 - 90.01: 3 90.01 - 114.77: 17321 114.77 - 139.53: 20310 139.53 - 164.28: 7 Bond angle restraints: 37646 Sorted by residual: angle pdb=" AO3 COA C2001 " pdb=" AP2 COA C2001 " pdb=" AO6 COA C2001 " ideal model delta sigma weight residual 102.60 40.50 62.10 3.00e+00 1.11e-01 4.29e+02 angle pdb=" AO3 COA D2001 " pdb=" AP1 COA D2001 " pdb="AO5* COA D2001 " ideal model delta sigma weight residual 102.60 46.20 56.40 3.00e+00 1.11e-01 3.53e+02 angle pdb=" AO4 COA D2001 " pdb=" AP2 COA D2001 " pdb=" AO6 COA D2001 " ideal model delta sigma weight residual 108.20 164.28 -56.08 3.00e+00 1.11e-01 3.49e+02 angle pdb=" AO2 COA C2001 " pdb=" AP1 COA C2001 " pdb="AO5* COA C2001 " ideal model delta sigma weight residual 109.50 56.62 52.88 3.00e+00 1.11e-01 3.11e+02 angle pdb=" AO3 COA D2001 " pdb=" AP2 COA D2001 " pdb=" AO6 COA D2001 " ideal model delta sigma weight residual 102.60 56.36 46.24 3.00e+00 1.11e-01 2.38e+02 ... (remaining 37641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 16408 35.99 - 71.99: 319 71.99 - 107.98: 35 107.98 - 143.98: 7 143.98 - 179.97: 5 Dihedral angle restraints: 16774 sinusoidal: 6759 harmonic: 10015 Sorted by residual: dihedral pdb=" CB CYS A 752 " pdb=" SG CYS A 752 " pdb=" SG CYS A 786 " pdb=" CB CYS A 786 " ideal model delta sinusoidal sigma weight residual 93.00 -176.53 -90.47 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS B 752 " pdb=" SG CYS B 752 " pdb=" SG CYS B 786 " pdb=" CB CYS B 786 " ideal model delta sinusoidal sigma weight residual 93.00 174.82 -81.82 1 1.00e+01 1.00e-02 8.23e+01 dihedral pdb=" CB CYS C 752 " pdb=" SG CYS C 752 " pdb=" SG CYS C 786 " pdb=" CB CYS C 786 " ideal model delta sinusoidal sigma weight residual 93.00 154.22 -61.22 1 1.00e+01 1.00e-02 4.98e+01 ... (remaining 16771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3661 0.074 - 0.147: 464 0.147 - 0.221: 25 0.221 - 0.294: 1 0.294 - 0.368: 2 Chirality restraints: 4153 Sorted by residual: chirality pdb=" CB VAL C 164 " pdb=" CA VAL C 164 " pdb=" CG1 VAL C 164 " pdb=" CG2 VAL C 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ILE C 239 " pdb=" N ILE C 239 " pdb=" C ILE C 239 " pdb=" CB ILE C 239 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4150 not shown) Planarity restraints: 4952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP C2000 " -0.181 2.00e-02 2.50e+03 5.85e-01 7.71e+03 pdb=" C2' ATP C2000 " 0.259 2.00e-02 2.50e+03 pdb=" C3' ATP C2000 " 0.599 2.00e-02 2.50e+03 pdb=" C4' ATP C2000 " -0.455 2.00e-02 2.50e+03 pdb=" C5' ATP C2000 " -0.007 2.00e-02 2.50e+03 pdb=" N9 ATP C2000 " 0.925 2.00e-02 2.50e+03 pdb=" O2' ATP C2000 " -0.768 2.00e-02 2.50e+03 pdb=" O3' ATP C2000 " 0.486 2.00e-02 2.50e+03 pdb=" O4' ATP C2000 " -0.858 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP D2002 " 0.190 2.00e-02 2.50e+03 5.85e-01 7.69e+03 pdb=" C2' ATP D2002 " -0.252 2.00e-02 2.50e+03 pdb=" C3' ATP D2002 " -0.607 2.00e-02 2.50e+03 pdb=" C4' ATP D2002 " 0.453 2.00e-02 2.50e+03 pdb=" C5' ATP D2002 " 0.014 2.00e-02 2.50e+03 pdb=" N9 ATP D2002 " -0.901 2.00e-02 2.50e+03 pdb=" O2' ATP D2002 " 0.827 2.00e-02 2.50e+03 pdb=" O3' ATP D2002 " -0.520 2.00e-02 2.50e+03 pdb=" O4' ATP D2002 " 0.798 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 199 " -0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C GLY C 199 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY C 199 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 200 " -0.024 2.00e-02 2.50e+03 ... (remaining 4949 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.77: 13 1.77 - 2.55: 366 2.55 - 3.34: 35383 3.34 - 4.12: 66547 4.12 - 4.90: 116395 Warning: very small nonbonded interaction distances. Nonbonded interactions: 218704 Sorted by model distance: nonbonded pdb=" NH2 ARG C 393 " pdb=" OE1 GLN C1075 " model vdw 0.990 2.520 nonbonded pdb=" NE2 GLN D 388 " pdb=" CG MET D1116 " model vdw 1.284 3.520 nonbonded pdb=" OE2 GLU C 395 " pdb=" N LEU C1088 " model vdw 1.323 2.520 nonbonded pdb=" CZ ARG C 453 " pdb=" NE2 GLN C 498 " model vdw 1.327 3.350 nonbonded pdb=" NE2 GLN C 78 " pdb=" OD1 ASN D1081 " model vdw 1.374 2.520 ... (remaining 218699 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 34 through 1178) selection = (chain 'D' and resid 34 through 1178) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.020 Extract box with map and model: 7.990 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 71.770 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.120 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:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 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 : 0.023 2.132 27745 Z= 1.171 Angle : 1.198 62.104 37646 Z= 0.523 Chirality : 0.047 0.368 4153 Planarity : 0.013 0.585 4952 Dihedral : 15.546 179.969 10336 Min Nonbonded Distance : 0.990 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 1.15 % Allowed : 0.87 % Favored : 97.98 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3483 helix: 0.63 (0.14), residues: 1407 sheet: -0.40 (0.24), residues: 471 loop : -1.77 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 624 HIS 0.019 0.001 HIS C 998 PHE 0.028 0.001 PHE A 876 TYR 0.023 0.002 TYR D 304 ARG 0.008 0.001 ARG D 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 535 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 502 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 LYS cc_start: 0.7347 (mttt) cc_final: 0.6917 (mttt) REVERT: A 641 MET cc_start: 0.6574 (ptp) cc_final: 0.6223 (ptt) REVERT: A 675 ARG cc_start: 0.6946 (ttm170) cc_final: 0.6222 (mtt-85) REVERT: A 686 MET cc_start: 0.9322 (mpp) cc_final: 0.9116 (mpp) REVERT: A 828 MET cc_start: 0.8521 (ttt) cc_final: 0.8279 (tpp) REVERT: A 986 ASP cc_start: 0.8679 (t0) cc_final: 0.8334 (t0) REVERT: A 992 LYS cc_start: 0.7461 (mmpt) cc_final: 0.7073 (mmtt) REVERT: B 504 LEU cc_start: 0.9080 (mm) cc_final: 0.8703 (pp) REVERT: B 724 MET cc_start: 0.9310 (mpp) cc_final: 0.8960 (mpp) REVERT: C 92 PRO cc_start: 0.9037 (Cg_exo) cc_final: 0.8679 (Cg_endo) REVERT: C 204 MET cc_start: 0.7231 (OUTLIER) cc_final: 0.5895 (mtt) REVERT: C 492 PRO cc_start: 0.7413 (Cg_endo) cc_final: 0.6527 (Cg_exo) REVERT: C 496 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7323 (mpp80) REVERT: C 502 HIS cc_start: 0.9031 (m90) cc_final: 0.8655 (m90) REVERT: C 686 MET cc_start: 0.8730 (mpp) cc_final: 0.7637 (mpp) REVERT: C 724 MET cc_start: 0.8872 (mmm) cc_final: 0.8449 (mmm) REVERT: C 754 MET cc_start: 0.9458 (pmm) cc_final: 0.9118 (pmm) REVERT: C 801 MET cc_start: 0.8127 (mpp) cc_final: 0.7721 (mpp) REVERT: C 854 MET cc_start: 0.7831 (mmm) cc_final: 0.7413 (mpp) REVERT: C 1032 SER cc_start: 0.8337 (m) cc_final: 0.8125 (t) REVERT: C 1038 PHE cc_start: 0.8563 (t80) cc_final: 0.8222 (t80) REVERT: C 1048 PHE cc_start: 0.8758 (p90) cc_final: 0.8484 (p90) REVERT: C 1098 MET cc_start: 0.7406 (tmm) cc_final: 0.7173 (tpp) REVERT: D 453 ARG cc_start: 0.4412 (OUTLIER) cc_final: 0.2005 (mmt180) REVERT: D 500 LEU cc_start: 0.9269 (mt) cc_final: 0.9055 (mm) REVERT: D 604 MET cc_start: 0.7219 (tpt) cc_final: 0.6670 (tpp) REVERT: D 641 MET cc_start: 0.6989 (ptm) cc_final: 0.5257 (tmm) REVERT: D 671 MET cc_start: 0.3812 (tpt) cc_final: 0.2996 (tpt) REVERT: D 784 LEU cc_start: 0.9233 (mm) cc_final: 0.8892 (pp) REVERT: D 920 PHE cc_start: 0.7319 (t80) cc_final: 0.7081 (t80) REVERT: D 1116 MET cc_start: 0.4981 (mpp) cc_final: 0.4673 (ptm) REVERT: D 1122 ASP cc_start: 0.8629 (m-30) cc_final: 0.8289 (p0) REVERT: D 1145 MET cc_start: 0.4614 (mtm) cc_final: 0.3340 (ttm) outliers start: 33 outliers final: 3 residues processed: 524 average time/residue: 0.4338 time to fit residues: 346.5845 Evaluate side-chains 309 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 303 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain D residue 453 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 0.9990 chunk 263 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 316 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 ASN ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 HIS ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN C 346 HIS ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN C 506 HIS C 560 HIS C 773 HIS ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 HIS D 463 GLN D 467 ASN D 494 GLN D 597 ASN ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 27745 Z= 0.280 Angle : 0.841 20.168 37646 Z= 0.392 Chirality : 0.046 0.319 4153 Planarity : 0.005 0.056 4952 Dihedral : 9.779 138.676 3894 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 2.13 % Allowed : 11.71 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.08 (0.14), residues: 3483 helix: 0.41 (0.13), residues: 1418 sheet: -0.54 (0.23), residues: 491 loop : -1.83 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 607 HIS 0.022 0.002 HIS B 879 PHE 0.027 0.002 PHE A 876 TYR 0.026 0.002 TYR B1013 ARG 0.008 0.001 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 379 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 318 time to evaluate : 2.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9320 (tp) cc_final: 0.9023 (pt) REVERT: A 566 MET cc_start: 0.6714 (ttp) cc_final: 0.5107 (ttp) REVERT: A 583 ARG cc_start: 0.8275 (ttt180) cc_final: 0.8013 (ttm170) REVERT: A 675 ARG cc_start: 0.7526 (ttm170) cc_final: 0.6689 (mtt180) REVERT: A 686 MET cc_start: 0.9261 (mpp) cc_final: 0.9052 (mpp) REVERT: A 743 MET cc_start: 0.7395 (tpt) cc_final: 0.6864 (tpp) REVERT: A 986 ASP cc_start: 0.8713 (t0) cc_final: 0.8380 (t0) REVERT: B 724 MET cc_start: 0.9531 (mpp) cc_final: 0.9293 (mpp) REVERT: B 828 MET cc_start: 0.8044 (ppp) cc_final: 0.7702 (ppp) REVERT: C 204 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6829 (mmp) REVERT: C 300 LYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7018 (pptt) REVERT: C 370 ASN cc_start: 0.4933 (p0) cc_final: 0.4633 (p0) REVERT: C 442 LYS cc_start: 0.8765 (mttt) cc_final: 0.8512 (mttt) REVERT: C 502 HIS cc_start: 0.9040 (m90) cc_final: 0.8729 (m90) REVERT: C 583 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.8081 (mtp180) REVERT: C 686 MET cc_start: 0.8887 (mpp) cc_final: 0.8014 (mpp) REVERT: C 724 MET cc_start: 0.9153 (mmm) cc_final: 0.8762 (mmm) REVERT: C 854 MET cc_start: 0.8251 (mmm) cc_final: 0.7788 (mpp) REVERT: C 874 LEU cc_start: 0.9064 (tp) cc_final: 0.8653 (mt) REVERT: C 1032 SER cc_start: 0.8537 (m) cc_final: 0.8207 (t) REVERT: C 1038 PHE cc_start: 0.8879 (t80) cc_final: 0.8480 (t80) REVERT: C 1048 PHE cc_start: 0.9095 (p90) cc_final: 0.8731 (p90) REVERT: C 1098 MET cc_start: 0.7386 (tmm) cc_final: 0.7160 (tpp) REVERT: D 453 ARG cc_start: 0.5142 (OUTLIER) cc_final: 0.4021 (mmt180) REVERT: D 500 LEU cc_start: 0.9182 (mt) cc_final: 0.8934 (mm) REVERT: D 604 MET cc_start: 0.7783 (tpt) cc_final: 0.6975 (tpp) REVERT: D 671 MET cc_start: 0.4394 (tpt) cc_final: 0.4119 (tpt) REVERT: D 728 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8794 (pt0) REVERT: D 743 MET cc_start: 0.7616 (mmp) cc_final: 0.7366 (mmm) REVERT: D 784 LEU cc_start: 0.9213 (mm) cc_final: 0.8856 (pp) REVERT: D 920 PHE cc_start: 0.7529 (t80) cc_final: 0.7104 (t80) REVERT: D 1122 ASP cc_start: 0.8597 (m-30) cc_final: 0.8280 (p0) REVERT: D 1143 MET cc_start: 0.0740 (mmp) cc_final: -0.0393 (mmm) REVERT: D 1145 MET cc_start: -0.0638 (mtm) cc_final: -0.1290 (ptp) REVERT: D 1166 MET cc_start: 0.7056 (tmm) cc_final: 0.6512 (ppp) outliers start: 61 outliers final: 32 residues processed: 360 average time/residue: 0.3921 time to fit residues: 223.9556 Evaluate side-chains 310 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 274 time to evaluate : 3.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1059 HIS Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 496 ARG Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 316 optimal weight: 0.4980 chunk 342 optimal weight: 6.9990 chunk 281 optimal weight: 0.0570 chunk 313 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 253 optimal weight: 20.0000 overall best weight: 1.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN ** B 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN C 44 ASN ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27745 Z= 0.189 Angle : 0.732 17.658 37646 Z= 0.337 Chirality : 0.044 0.241 4153 Planarity : 0.004 0.065 4952 Dihedral : 9.628 155.532 3890 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.92 % Favored : 93.02 % Rotamer: Outliers : 2.65 % Allowed : 15.06 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.95 (0.14), residues: 3483 helix: 0.50 (0.14), residues: 1436 sheet: -0.45 (0.24), residues: 483 loop : -1.77 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 624 HIS 0.014 0.001 HIS A 998 PHE 0.027 0.001 PHE A 876 TYR 0.024 0.002 TYR D 422 ARG 0.013 0.001 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 360 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 284 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9345 (tp) cc_final: 0.9051 (pt) REVERT: A 583 ARG cc_start: 0.8279 (ttt180) cc_final: 0.7727 (ttt180) REVERT: A 641 MET cc_start: 0.5629 (ptm) cc_final: 0.4898 (ptt) REVERT: A 675 ARG cc_start: 0.7520 (ttm170) cc_final: 0.6595 (mtm-85) REVERT: A 743 MET cc_start: 0.7584 (tpt) cc_final: 0.7297 (tpp) REVERT: A 986 ASP cc_start: 0.8703 (t0) cc_final: 0.8370 (t0) REVERT: B 828 MET cc_start: 0.7996 (ppp) cc_final: 0.7780 (ppp) REVERT: B 891 LYS cc_start: 0.6380 (OUTLIER) cc_final: 0.5995 (mttp) REVERT: C 70 GLN cc_start: 0.8677 (pm20) cc_final: 0.8310 (pm20) REVERT: C 84 TYR cc_start: 0.4061 (OUTLIER) cc_final: 0.3587 (m-80) REVERT: C 120 PHE cc_start: 0.5252 (OUTLIER) cc_final: 0.4851 (m-10) REVERT: C 300 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6905 (pptt) REVERT: C 370 ASN cc_start: 0.4911 (p0) cc_final: 0.4620 (p0) REVERT: C 502 HIS cc_start: 0.9006 (m90) cc_final: 0.8741 (m90) REVERT: C 583 ARG cc_start: 0.8403 (ttt-90) cc_final: 0.8019 (mtp180) REVERT: C 604 MET cc_start: 0.8213 (mmm) cc_final: 0.7415 (tpp) REVERT: C 686 MET cc_start: 0.8810 (mpp) cc_final: 0.8241 (mpp) REVERT: C 690 MET cc_start: 0.8645 (mpp) cc_final: 0.8381 (mpp) REVERT: C 724 MET cc_start: 0.9135 (mmm) cc_final: 0.8728 (mmm) REVERT: C 854 MET cc_start: 0.8296 (mmm) cc_final: 0.8081 (mpp) REVERT: C 1012 MET cc_start: 0.7921 (ptt) cc_final: 0.7538 (ptp) REVERT: C 1032 SER cc_start: 0.8664 (m) cc_final: 0.8314 (t) REVERT: C 1038 PHE cc_start: 0.8812 (t80) cc_final: 0.8367 (t80) REVERT: C 1048 PHE cc_start: 0.9094 (p90) cc_final: 0.8781 (p90) REVERT: D 348 GLN cc_start: 0.5976 (OUTLIER) cc_final: 0.5667 (tt0) REVERT: D 453 ARG cc_start: 0.4791 (OUTLIER) cc_final: 0.3881 (mmm-85) REVERT: D 500 LEU cc_start: 0.9139 (mt) cc_final: 0.8903 (mm) REVERT: D 604 MET cc_start: 0.7705 (tpt) cc_final: 0.6794 (tpp) REVERT: D 641 MET cc_start: 0.6698 (tmm) cc_final: 0.5851 (tmm) REVERT: D 743 MET cc_start: 0.7519 (mmp) cc_final: 0.7286 (mmm) REVERT: D 784 LEU cc_start: 0.9157 (mm) cc_final: 0.8838 (pp) REVERT: D 920 PHE cc_start: 0.7544 (t80) cc_final: 0.6971 (t80) REVERT: D 1122 ASP cc_start: 0.8592 (m-30) cc_final: 0.8291 (p0) REVERT: D 1143 MET cc_start: 0.0780 (mmp) cc_final: -0.0358 (mmm) REVERT: D 1145 MET cc_start: -0.0648 (mtm) cc_final: -0.1190 (ptm) REVERT: D 1166 MET cc_start: 0.7127 (tmm) cc_final: 0.6336 (ppp) outliers start: 76 outliers final: 43 residues processed: 340 average time/residue: 0.3834 time to fit residues: 210.0585 Evaluate side-chains 318 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 891 LYS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1090 LYS Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 1049 GLU Chi-restraints excluded: chain D residue 1063 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 0.8980 chunk 238 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 212 optimal weight: 0.0770 chunk 317 optimal weight: 0.5980 chunk 336 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 301 optimal weight: 0.0170 chunk 90 optimal weight: 0.0870 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 771 HIS C 216 ASN ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27745 Z= 0.160 Angle : 0.712 17.114 37646 Z= 0.323 Chirality : 0.043 0.223 4153 Planarity : 0.004 0.047 4952 Dihedral : 8.920 157.000 3886 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.60 % Favored : 93.31 % Rotamer: Outliers : 2.37 % Allowed : 16.38 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.92 (0.14), residues: 3483 helix: 0.49 (0.14), residues: 1443 sheet: -0.37 (0.25), residues: 455 loop : -1.73 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 624 HIS 0.019 0.001 HIS A 506 PHE 0.026 0.001 PHE A 876 TYR 0.024 0.001 TYR B1013 ARG 0.010 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 359 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 291 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9364 (tp) cc_final: 0.9080 (pt) REVERT: A 566 MET cc_start: 0.5951 (ttp) cc_final: 0.4184 (ttp) REVERT: A 583 ARG cc_start: 0.8261 (ttt180) cc_final: 0.7849 (ttm-80) REVERT: A 604 MET cc_start: 0.2892 (ppp) cc_final: 0.2602 (ppp) REVERT: A 641 MET cc_start: 0.6266 (ptm) cc_final: 0.5524 (ptt) REVERT: A 675 ARG cc_start: 0.7413 (ttm170) cc_final: 0.6541 (mtm-85) REVERT: A 986 ASP cc_start: 0.8612 (t0) cc_final: 0.8228 (t0) REVERT: B 724 MET cc_start: 0.9554 (mpp) cc_final: 0.9346 (mpp) REVERT: B 754 MET cc_start: 0.9124 (mmm) cc_final: 0.8870 (mmm) REVERT: B 891 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.6048 (mttp) REVERT: C 70 GLN cc_start: 0.8532 (pm20) cc_final: 0.8130 (pm20) REVERT: C 79 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.4968 (ptmm) REVERT: C 204 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6621 (mmp) REVERT: C 300 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6793 (pptt) REVERT: C 370 ASN cc_start: 0.4750 (p0) cc_final: 0.4472 (p0) REVERT: C 502 HIS cc_start: 0.9022 (m90) cc_final: 0.8694 (m90) REVERT: C 583 ARG cc_start: 0.8256 (ttt-90) cc_final: 0.7980 (mtp180) REVERT: C 686 MET cc_start: 0.8696 (mpp) cc_final: 0.8138 (mpp) REVERT: C 724 MET cc_start: 0.9125 (mmm) cc_final: 0.8645 (mmm) REVERT: C 874 LEU cc_start: 0.9042 (tp) cc_final: 0.8627 (mt) REVERT: C 1032 SER cc_start: 0.8614 (m) cc_final: 0.8169 (t) REVERT: C 1038 PHE cc_start: 0.8772 (t80) cc_final: 0.8315 (t80) REVERT: C 1048 PHE cc_start: 0.9053 (p90) cc_final: 0.8793 (p90) REVERT: C 1051 GLU cc_start: 0.8236 (tp30) cc_final: 0.7957 (tp30) REVERT: C 1087 ILE cc_start: 0.8908 (mm) cc_final: 0.8546 (tp) REVERT: D 38 LYS cc_start: 0.7555 (pttm) cc_final: 0.7318 (pttm) REVERT: D 268 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.6673 (mm110) REVERT: D 348 GLN cc_start: 0.6172 (OUTLIER) cc_final: 0.5707 (tt0) REVERT: D 604 MET cc_start: 0.7687 (tpt) cc_final: 0.6878 (tpp) REVERT: D 641 MET cc_start: 0.6099 (tmm) cc_final: 0.5501 (tmm) REVERT: D 728 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8763 (pt0) REVERT: D 743 MET cc_start: 0.7385 (mmp) cc_final: 0.7163 (mmm) REVERT: D 784 LEU cc_start: 0.9111 (mm) cc_final: 0.8809 (pp) REVERT: D 804 MET cc_start: 0.8308 (mmp) cc_final: 0.8010 (mmp) REVERT: D 920 PHE cc_start: 0.7510 (t80) cc_final: 0.7101 (t80) REVERT: D 1012 MET cc_start: 0.8772 (mpp) cc_final: 0.8031 (mpp) REVERT: D 1122 ASP cc_start: 0.8619 (m-30) cc_final: 0.8319 (p0) REVERT: D 1143 MET cc_start: 0.0743 (mmp) cc_final: -0.0364 (mmm) REVERT: D 1145 MET cc_start: -0.1150 (mtm) cc_final: -0.1680 (ptp) REVERT: D 1166 MET cc_start: 0.6674 (tmm) cc_final: 0.5788 (ppp) outliers start: 68 outliers final: 37 residues processed: 337 average time/residue: 0.3775 time to fit residues: 203.9325 Evaluate side-chains 314 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 270 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1077 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 891 LYS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 421 HIS Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 729 GLU Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 250 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 287 optimal weight: 8.9990 chunk 232 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 301 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 181 HIS ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN ** C 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 560 HIS ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN D 467 ASN ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 GLN ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 924 ASN ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1111 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27745 Z= 0.292 Angle : 0.789 18.298 37646 Z= 0.382 Chirality : 0.045 0.246 4153 Planarity : 0.005 0.061 4952 Dihedral : 8.995 166.303 3884 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 26.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.81 % Favored : 92.13 % Rotamer: Outliers : 3.80 % Allowed : 18.09 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.22 (0.14), residues: 3483 helix: 0.17 (0.13), residues: 1429 sheet: -0.66 (0.23), residues: 480 loop : -1.77 (0.15), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 838 HIS 0.019 0.002 HIS A 998 PHE 0.023 0.002 PHE C 471 TYR 0.022 0.002 TYR C 620 ARG 0.011 0.001 ARG C 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 373 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 264 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9400 (tp) cc_final: 0.9016 (pt) REVERT: A 583 ARG cc_start: 0.8618 (ttt180) cc_final: 0.8363 (ttm170) REVERT: A 604 MET cc_start: 0.3746 (ppp) cc_final: 0.3186 (ppp) REVERT: A 675 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7042 (mtm-85) REVERT: A 920 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8979 (m-10) REVERT: A 986 ASP cc_start: 0.8539 (t0) cc_final: 0.8202 (t0) REVERT: B 724 MET cc_start: 0.9601 (mpp) cc_final: 0.9299 (mpp) REVERT: B 754 MET cc_start: 0.9195 (mmm) cc_final: 0.8884 (mmm) REVERT: C 70 GLN cc_start: 0.8541 (pm20) cc_final: 0.8137 (pm20) REVERT: C 79 LYS cc_start: 0.6945 (OUTLIER) cc_final: 0.6021 (ptmm) REVERT: C 84 TYR cc_start: 0.4438 (OUTLIER) cc_final: 0.3843 (m-80) REVERT: C 204 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6720 (mmp) REVERT: C 300 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7064 (pptt) REVERT: C 502 HIS cc_start: 0.9165 (m90) cc_final: 0.8792 (m90) REVERT: C 641 MET cc_start: 0.7196 (mtm) cc_final: 0.6792 (mtm) REVERT: C 686 MET cc_start: 0.8863 (mpp) cc_final: 0.8254 (mpp) REVERT: C 724 MET cc_start: 0.9232 (mmm) cc_final: 0.8821 (mmm) REVERT: C 1038 PHE cc_start: 0.8885 (t80) cc_final: 0.8498 (t80) REVERT: C 1048 PHE cc_start: 0.9217 (p90) cc_final: 0.8980 (p90) REVERT: D 268 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7146 (mm-40) REVERT: D 294 ASP cc_start: 0.6712 (m-30) cc_final: 0.6496 (t0) REVERT: D 374 ILE cc_start: 0.8677 (mm) cc_final: 0.8428 (tp) REVERT: D 453 ARG cc_start: 0.5102 (OUTLIER) cc_final: 0.4176 (mtm-85) REVERT: D 508 MET cc_start: 0.9312 (ptp) cc_final: 0.9004 (ptp) REVERT: D 604 MET cc_start: 0.8000 (tpt) cc_final: 0.7267 (tpp) REVERT: D 641 MET cc_start: 0.6295 (tmm) cc_final: 0.5849 (tmm) REVERT: D 724 MET cc_start: 0.8937 (mmm) cc_final: 0.8498 (mmm) REVERT: D 728 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8672 (mp0) REVERT: D 743 MET cc_start: 0.7407 (mmp) cc_final: 0.7104 (mmm) REVERT: D 784 LEU cc_start: 0.9119 (mm) cc_final: 0.8734 (pp) REVERT: D 804 MET cc_start: 0.8537 (mmp) cc_final: 0.8166 (mmp) REVERT: D 920 PHE cc_start: 0.7786 (t80) cc_final: 0.7344 (t80) REVERT: D 1012 MET cc_start: 0.9014 (mpp) cc_final: 0.8794 (mpp) REVERT: D 1116 MET cc_start: 0.7813 (mpp) cc_final: 0.7537 (mtt) REVERT: D 1122 ASP cc_start: 0.8589 (m-30) cc_final: 0.8321 (p0) REVERT: D 1143 MET cc_start: 0.0981 (mmp) cc_final: -0.0315 (mmm) REVERT: D 1166 MET cc_start: 0.6869 (tmm) cc_final: 0.5972 (ppp) outliers start: 109 outliers final: 64 residues processed: 342 average time/residue: 0.3678 time to fit residues: 205.7691 Evaluate side-chains 325 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 253 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1007 VAL Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 79 LYS Chi-restraints excluded: chain C residue 84 TYR Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1037 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 390 ASP Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 465 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 20.0000 chunk 302 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 336 optimal weight: 9.9990 chunk 279 optimal weight: 20.0000 chunk 155 optimal weight: 0.0170 chunk 27 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 overall best weight: 4.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 ASN C1040 GLN ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 HIS ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 873 ASN ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1034 ASN ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27745 Z= 0.257 Angle : 0.761 17.709 37646 Z= 0.360 Chirality : 0.044 0.241 4153 Planarity : 0.005 0.056 4952 Dihedral : 8.874 177.873 3884 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.35 % Favored : 92.59 % Rotamer: Outliers : 3.24 % Allowed : 19.80 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.21 (0.14), residues: 3483 helix: 0.18 (0.14), residues: 1430 sheet: -0.65 (0.24), residues: 449 loop : -1.75 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 838 HIS 0.042 0.002 HIS C 76 PHE 0.024 0.002 PHE C 471 TYR 0.026 0.002 TYR D 422 ARG 0.028 0.001 ARG B 547 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 356 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 263 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9350 (tp) cc_final: 0.9021 (pt) REVERT: A 566 MET cc_start: 0.6422 (ttp) cc_final: 0.5095 (ttm) REVERT: A 583 ARG cc_start: 0.8726 (ttt180) cc_final: 0.8215 (ttm-80) REVERT: A 671 MET cc_start: 0.5072 (ttt) cc_final: 0.4494 (ttt) REVERT: A 675 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7134 (mtt180) REVERT: A 920 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8981 (m-10) REVERT: A 986 ASP cc_start: 0.8455 (t0) cc_final: 0.8133 (t0) REVERT: B 724 MET cc_start: 0.9584 (mpp) cc_final: 0.9359 (mpp) REVERT: B 754 MET cc_start: 0.9247 (mmm) cc_final: 0.8888 (mmm) REVERT: C 70 GLN cc_start: 0.8500 (pm20) cc_final: 0.8235 (pm20) REVERT: C 204 MET cc_start: 0.7030 (tpt) cc_final: 0.6648 (mmp) REVERT: C 300 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7108 (pptt) REVERT: C 502 HIS cc_start: 0.9048 (m90) cc_final: 0.8759 (m90) REVERT: C 663 CYS cc_start: 0.8272 (m) cc_final: 0.7261 (p) REVERT: C 671 MET cc_start: 0.2237 (tpt) cc_final: 0.2015 (tpt) REVERT: C 686 MET cc_start: 0.8904 (mpp) cc_final: 0.7995 (mpp) REVERT: C 724 MET cc_start: 0.9242 (mmm) cc_final: 0.8828 (mmm) REVERT: C 1038 PHE cc_start: 0.8856 (t80) cc_final: 0.8478 (t80) REVERT: C 1048 PHE cc_start: 0.9150 (p90) cc_final: 0.8780 (p90) REVERT: D 38 LYS cc_start: 0.7785 (pttm) cc_final: 0.7492 (pttm) REVERT: D 204 MET cc_start: 0.7664 (tmm) cc_final: 0.7433 (mpp) REVERT: D 268 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7902 (mm-40) REVERT: D 508 MET cc_start: 0.9292 (ptp) cc_final: 0.9050 (ptp) REVERT: D 586 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7018 (p0) REVERT: D 604 MET cc_start: 0.8005 (tpt) cc_final: 0.7246 (tpp) REVERT: D 641 MET cc_start: 0.6214 (tmm) cc_final: 0.5815 (tmm) REVERT: D 721 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8884 (pm20) REVERT: D 743 MET cc_start: 0.7405 (mmp) cc_final: 0.7090 (mmm) REVERT: D 784 LEU cc_start: 0.9146 (mm) cc_final: 0.8747 (pp) REVERT: D 804 MET cc_start: 0.8498 (mmp) cc_final: 0.7989 (mmp) REVERT: D 848 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5562 (p90) REVERT: D 920 PHE cc_start: 0.7907 (t80) cc_final: 0.7607 (t80) REVERT: D 1081 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6756 (m-40) REVERT: D 1116 MET cc_start: 0.8035 (mpp) cc_final: 0.7211 (mtm) REVERT: D 1122 ASP cc_start: 0.8590 (m-30) cc_final: 0.8354 (p0) REVERT: D 1143 MET cc_start: 0.1127 (mmp) cc_final: -0.0184 (mmm) REVERT: D 1166 MET cc_start: 0.6867 (tmm) cc_final: 0.6046 (ppp) outliers start: 93 outliers final: 65 residues processed: 334 average time/residue: 0.3712 time to fit residues: 204.8111 Evaluate side-chains 325 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 253 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 685 ASN Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain D residue 728 GLU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 944 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1034 ASN Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1081 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 191 optimal weight: 0.0010 chunk 245 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 283 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 335 optimal weight: 4.9990 chunk 209 optimal weight: 0.9980 chunk 204 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS C 248 GLN ** C 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 721 GLN ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1040 GLN ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 27745 Z= 0.273 Angle : 0.778 17.968 37646 Z= 0.372 Chirality : 0.045 0.342 4153 Planarity : 0.005 0.043 4952 Dihedral : 8.649 153.936 3881 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 26.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.04 % Favored : 91.87 % Rotamer: Outliers : 3.97 % Allowed : 20.04 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.37 (0.14), residues: 3483 helix: 0.01 (0.13), residues: 1429 sheet: -0.78 (0.24), residues: 462 loop : -1.79 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 607 HIS 0.019 0.002 HIS C 76 PHE 0.025 0.002 PHE C 471 TYR 0.021 0.002 TYR B1013 ARG 0.013 0.001 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 365 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 251 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9343 (tp) cc_final: 0.8977 (pt) REVERT: A 583 ARG cc_start: 0.8688 (ttt180) cc_final: 0.7998 (ttt180) REVERT: A 604 MET cc_start: 0.3586 (ppp) cc_final: 0.2640 (ppp) REVERT: A 675 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7238 (mtm-85) REVERT: A 920 PHE cc_start: 0.9260 (OUTLIER) cc_final: 0.8979 (m-10) REVERT: B 724 MET cc_start: 0.9592 (mpp) cc_final: 0.9367 (mpp) REVERT: B 754 MET cc_start: 0.9299 (mmm) cc_final: 0.8918 (mmm) REVERT: C 70 GLN cc_start: 0.8517 (pm20) cc_final: 0.8221 (pm20) REVERT: C 300 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7126 (pptt) REVERT: C 502 HIS cc_start: 0.9121 (m90) cc_final: 0.8803 (m90) REVERT: C 686 MET cc_start: 0.8840 (mpp) cc_final: 0.7873 (mpp) REVERT: C 724 MET cc_start: 0.9272 (mmm) cc_final: 0.8897 (mmm) REVERT: C 1022 ASP cc_start: 0.7837 (m-30) cc_final: 0.6680 (p0) REVERT: C 1038 PHE cc_start: 0.8879 (t80) cc_final: 0.8564 (t80) REVERT: C 1048 PHE cc_start: 0.9162 (p90) cc_final: 0.8799 (p90) REVERT: D 268 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: D 337 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7525 (tm-30) REVERT: D 566 MET cc_start: 0.5920 (tmm) cc_final: 0.5684 (tmm) REVERT: D 604 MET cc_start: 0.8138 (tpt) cc_final: 0.7420 (tpp) REVERT: D 641 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5942 (tmm) REVERT: D 784 LEU cc_start: 0.9066 (mm) cc_final: 0.8638 (pp) REVERT: D 804 MET cc_start: 0.8521 (mmp) cc_final: 0.8022 (mmp) REVERT: D 820 THR cc_start: 0.6736 (m) cc_final: 0.6490 (t) REVERT: D 848 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5839 (p90) REVERT: D 920 PHE cc_start: 0.8020 (t80) cc_final: 0.7760 (t80) REVERT: D 1034 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.8222 (p0) REVERT: D 1081 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6860 (m-40) REVERT: D 1116 MET cc_start: 0.7879 (mpp) cc_final: 0.7422 (mtm) REVERT: D 1122 ASP cc_start: 0.8606 (m-30) cc_final: 0.8378 (p0) REVERT: D 1143 MET cc_start: 0.1637 (mmp) cc_final: 0.0413 (mmm) REVERT: D 1166 MET cc_start: 0.6665 (tmm) cc_final: 0.5789 (ppp) outliers start: 114 outliers final: 84 residues processed: 338 average time/residue: 0.3632 time to fit residues: 200.5920 Evaluate side-chains 338 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 246 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 910 SER Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain B residue 510 ASN Chi-restraints excluded: chain B residue 543 ASP Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1030 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 518 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 674 PHE Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 88 ARG Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 641 MET Chi-restraints excluded: chain D residue 721 GLN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 944 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1007 VAL Chi-restraints excluded: chain D residue 1034 ASN Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1081 ASN Chi-restraints excluded: chain D residue 1089 VAL Chi-restraints excluded: chain D residue 1157 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 3.9990 chunk 133 optimal weight: 0.0000 chunk 200 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 65 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 overall best weight: 1.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS D 721 GLN ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 27745 Z= 0.182 Angle : 0.743 17.229 37646 Z= 0.342 Chirality : 0.044 0.164 4153 Planarity : 0.004 0.045 4952 Dihedral : 8.322 141.983 3881 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.92 % Favored : 93.02 % Rotamer: Outliers : 3.03 % Allowed : 21.23 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.14), residues: 3483 helix: 0.24 (0.14), residues: 1434 sheet: -0.57 (0.24), residues: 452 loop : -1.72 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 624 HIS 0.012 0.001 HIS A 506 PHE 0.030 0.002 PHE A 963 TYR 0.023 0.001 TYR B1013 ARG 0.010 0.001 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 341 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 254 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9295 (tp) cc_final: 0.8999 (pt) REVERT: A 583 ARG cc_start: 0.8635 (ttt180) cc_final: 0.8267 (ttt180) REVERT: A 604 MET cc_start: 0.3183 (ppp) cc_final: 0.2346 (ppp) REVERT: A 606 ASN cc_start: 0.5186 (OUTLIER) cc_final: 0.4454 (p0) REVERT: A 675 ARG cc_start: 0.8010 (ttm170) cc_final: 0.7145 (mtm-85) REVERT: A 920 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8997 (m-10) REVERT: A 986 ASP cc_start: 0.8531 (t0) cc_final: 0.8228 (t0) REVERT: B 754 MET cc_start: 0.9302 (mmm) cc_final: 0.8903 (mmm) REVERT: B 828 MET cc_start: 0.7828 (ppp) cc_final: 0.7617 (ppp) REVERT: C 70 GLN cc_start: 0.8535 (pm20) cc_final: 0.8252 (pm20) REVERT: C 300 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7128 (pptt) REVERT: C 502 HIS cc_start: 0.9068 (m90) cc_final: 0.8752 (m90) REVERT: C 686 MET cc_start: 0.8931 (mpp) cc_final: 0.7933 (mpp) REVERT: C 724 MET cc_start: 0.9239 (mmm) cc_final: 0.8855 (mmm) REVERT: C 1022 ASP cc_start: 0.7785 (m-30) cc_final: 0.6654 (p0) REVERT: C 1038 PHE cc_start: 0.8881 (t80) cc_final: 0.8605 (t80) REVERT: C 1048 PHE cc_start: 0.9075 (p90) cc_final: 0.8697 (p90) REVERT: D 38 LYS cc_start: 0.7829 (pttm) cc_final: 0.7567 (pttm) REVERT: D 261 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6341 (m-10) REVERT: D 268 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7607 (tt0) REVERT: D 337 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7444 (tm-30) REVERT: D 452 VAL cc_start: 0.8262 (OUTLIER) cc_final: 0.8059 (m) REVERT: D 453 ARG cc_start: 0.5385 (OUTLIER) cc_final: 0.4877 (mtt-85) REVERT: D 500 LEU cc_start: 0.9140 (mm) cc_final: 0.8709 (mm) REVERT: D 508 MET cc_start: 0.9263 (ptp) cc_final: 0.8891 (ptp) REVERT: D 604 MET cc_start: 0.8200 (tpt) cc_final: 0.7445 (tpp) REVERT: D 641 MET cc_start: 0.6280 (OUTLIER) cc_final: 0.5740 (tmm) REVERT: D 743 MET cc_start: 0.7279 (mmp) cc_final: 0.6948 (mmm) REVERT: D 784 LEU cc_start: 0.9039 (mm) cc_final: 0.8623 (pp) REVERT: D 804 MET cc_start: 0.8395 (mmp) cc_final: 0.7957 (mmp) REVERT: D 820 THR cc_start: 0.6737 (m) cc_final: 0.6457 (t) REVERT: D 848 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5379 (p90) REVERT: D 1012 MET cc_start: 0.8948 (mpp) cc_final: 0.8604 (mpp) REVERT: D 1081 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6680 (m-40) REVERT: D 1116 MET cc_start: 0.7791 (mpp) cc_final: 0.7224 (mtp) REVERT: D 1122 ASP cc_start: 0.8619 (m-30) cc_final: 0.8378 (p0) REVERT: D 1143 MET cc_start: 0.0972 (mmp) cc_final: -0.0208 (mmm) REVERT: D 1166 MET cc_start: 0.6919 (tmm) cc_final: 0.6118 (ppp) outliers start: 87 outliers final: 67 residues processed: 318 average time/residue: 0.3719 time to fit residues: 194.1599 Evaluate side-chains 324 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 246 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1116 MET Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 333 HIS Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 453 ARG Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 641 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 944 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1081 ASN Chi-restraints excluded: chain D residue 1157 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 6.9990 chunk 321 optimal weight: 4.9990 chunk 293 optimal weight: 6.9990 chunk 312 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 136 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 chunk 95 optimal weight: 0.4980 chunk 282 optimal weight: 0.0670 chunk 295 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 overall best weight: 3.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 129 GLN ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 27745 Z= 0.263 Angle : 0.792 17.484 37646 Z= 0.376 Chirality : 0.045 0.344 4153 Planarity : 0.005 0.077 4952 Dihedral : 8.319 143.363 3881 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 26.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.24 % Favored : 91.67 % Rotamer: Outliers : 3.28 % Allowed : 21.33 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.33 (0.14), residues: 3483 helix: 0.09 (0.14), residues: 1432 sheet: -0.77 (0.24), residues: 462 loop : -1.83 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 838 HIS 0.023 0.002 HIS D 333 PHE 0.074 0.002 PHE D 53 TYR 0.024 0.002 TYR B1013 ARG 0.013 0.001 ARG C 385 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 347 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 253 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9278 (tp) cc_final: 0.8964 (pt) REVERT: A 675 ARG cc_start: 0.8120 (ttm170) cc_final: 0.7311 (mtm180) REVERT: A 920 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8974 (m-10) REVERT: A 986 ASP cc_start: 0.8470 (t0) cc_final: 0.8191 (t0) REVERT: A 1043 LYS cc_start: 0.8864 (pttm) cc_final: 0.8605 (pptt) REVERT: B 754 MET cc_start: 0.9335 (mmm) cc_final: 0.8966 (mmm) REVERT: C 70 GLN cc_start: 0.8564 (pm20) cc_final: 0.8259 (pm20) REVERT: C 204 MET cc_start: 0.6813 (tpt) cc_final: 0.6102 (mmp) REVERT: C 300 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7195 (pptt) REVERT: C 502 HIS cc_start: 0.9115 (m90) cc_final: 0.8807 (m90) REVERT: C 686 MET cc_start: 0.9009 (mpp) cc_final: 0.8021 (mpp) REVERT: C 724 MET cc_start: 0.9278 (mmm) cc_final: 0.8901 (mmm) REVERT: C 801 MET cc_start: 0.7666 (pmm) cc_final: 0.7407 (pmm) REVERT: C 1022 ASP cc_start: 0.7867 (m-30) cc_final: 0.6732 (p0) REVERT: C 1048 PHE cc_start: 0.9162 (p90) cc_final: 0.8812 (p90) REVERT: D 38 LYS cc_start: 0.7852 (pttm) cc_final: 0.7600 (pttm) REVERT: D 204 MET cc_start: 0.7584 (tmm) cc_final: 0.7111 (mpp) REVERT: D 268 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7718 (tt0) REVERT: D 337 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: D 452 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8288 (m) REVERT: D 500 LEU cc_start: 0.9172 (mm) cc_final: 0.8762 (mm) REVERT: D 508 MET cc_start: 0.9338 (ptp) cc_final: 0.8973 (ptp) REVERT: D 604 MET cc_start: 0.8234 (tpt) cc_final: 0.7440 (tpp) REVERT: D 641 MET cc_start: 0.6390 (tmm) cc_final: 0.6124 (tmm) REVERT: D 784 LEU cc_start: 0.9071 (mm) cc_final: 0.8652 (pp) REVERT: D 804 MET cc_start: 0.8516 (mmp) cc_final: 0.8131 (mmp) REVERT: D 820 THR cc_start: 0.6928 (m) cc_final: 0.6656 (t) REVERT: D 848 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.5810 (p90) REVERT: D 1012 MET cc_start: 0.9054 (mpp) cc_final: 0.8559 (mpp) REVERT: D 1081 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6930 (m-40) REVERT: D 1116 MET cc_start: 0.7816 (mpp) cc_final: 0.7313 (mtp) REVERT: D 1122 ASP cc_start: 0.8573 (m-30) cc_final: 0.8366 (p0) REVERT: D 1143 MET cc_start: 0.1270 (mmp) cc_final: 0.0027 (mmm) outliers start: 94 outliers final: 77 residues processed: 323 average time/residue: 0.3702 time to fit residues: 197.3226 Evaluate side-chains 332 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 248 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1060 ILE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 662 PHE Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1030 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 372 CYS Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 586 ASP Chi-restraints excluded: chain D residue 616 MET Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 810 MET Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 944 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1081 ASN Chi-restraints excluded: chain D residue 1157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.0060 chunk 330 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 229 optimal weight: 30.0000 chunk 346 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.151 27745 Z= 0.191 Angle : 0.759 17.243 37646 Z= 0.351 Chirality : 0.044 0.197 4153 Planarity : 0.005 0.062 4952 Dihedral : 8.039 142.743 3877 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.09 % Favored : 92.82 % Rotamer: Outliers : 2.72 % Allowed : 21.92 % Favored : 75.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.19 (0.14), residues: 3483 helix: 0.26 (0.14), residues: 1435 sheet: -0.71 (0.24), residues: 456 loop : -1.80 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 624 HIS 0.012 0.001 HIS A 506 PHE 0.086 0.002 PHE D 53 TYR 0.034 0.002 TYR C 706 ARG 0.012 0.001 ARG C 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6966 Ramachandran restraints generated. 3483 Oldfield, 0 Emsley, 3483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** WARNING: vdw radius undefined for: (HS1 HS); setting to: 1.0 Evaluate side-chains 332 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 254 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LEU cc_start: 0.9287 (tp) cc_final: 0.8976 (pt) REVERT: A 583 ARG cc_start: 0.8532 (ttt180) cc_final: 0.7650 (ttt180) REVERT: A 604 MET cc_start: 0.3869 (ppp) cc_final: 0.3161 (ppp) REVERT: A 675 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7248 (mtm180) REVERT: A 920 PHE cc_start: 0.9292 (OUTLIER) cc_final: 0.8991 (m-10) REVERT: A 986 ASP cc_start: 0.8644 (t0) cc_final: 0.8370 (t0) REVERT: A 1043 LYS cc_start: 0.8812 (pttm) cc_final: 0.8536 (pptt) REVERT: B 754 MET cc_start: 0.9332 (mmm) cc_final: 0.8981 (mmm) REVERT: C 70 GLN cc_start: 0.8499 (pm20) cc_final: 0.8225 (pm20) REVERT: C 300 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7208 (pptt) REVERT: C 502 HIS cc_start: 0.9075 (m90) cc_final: 0.8768 (m90) REVERT: C 686 MET cc_start: 0.9020 (mpp) cc_final: 0.8043 (mpp) REVERT: C 724 MET cc_start: 0.9246 (mmm) cc_final: 0.8880 (mmm) REVERT: C 801 MET cc_start: 0.7682 (pmm) cc_final: 0.7445 (pmm) REVERT: C 1022 ASP cc_start: 0.7910 (m-30) cc_final: 0.6860 (p0) REVERT: C 1048 PHE cc_start: 0.9061 (p90) cc_final: 0.8730 (p90) REVERT: D 38 LYS cc_start: 0.7776 (pttm) cc_final: 0.7540 (pttm) REVERT: D 204 MET cc_start: 0.7515 (tmm) cc_final: 0.7032 (mpp) REVERT: D 261 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6549 (m-10) REVERT: D 337 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7676 (tp30) REVERT: D 374 ILE cc_start: 0.8604 (mm) cc_final: 0.8343 (tp) REVERT: D 500 LEU cc_start: 0.9189 (mm) cc_final: 0.8792 (mm) REVERT: D 604 MET cc_start: 0.8205 (tpt) cc_final: 0.7439 (tpp) REVERT: D 641 MET cc_start: 0.6216 (tmm) cc_final: 0.5695 (tmm) REVERT: D 743 MET cc_start: 0.7353 (mmp) cc_final: 0.6994 (mmm) REVERT: D 784 LEU cc_start: 0.9121 (mm) cc_final: 0.8621 (pp) REVERT: D 804 MET cc_start: 0.8445 (mmp) cc_final: 0.8014 (mmp) REVERT: D 820 THR cc_start: 0.6976 (m) cc_final: 0.6702 (t) REVERT: D 848 PHE cc_start: 0.6552 (OUTLIER) cc_final: 0.5501 (p90) REVERT: D 1012 MET cc_start: 0.9035 (mpp) cc_final: 0.8540 (mpp) REVERT: D 1116 MET cc_start: 0.7733 (mpp) cc_final: 0.7047 (mtp) REVERT: D 1122 ASP cc_start: 0.8575 (m-30) cc_final: 0.8372 (p0) REVERT: D 1166 MET cc_start: 0.5913 (ppp) cc_final: 0.5006 (ppp) outliers start: 78 outliers final: 63 residues processed: 312 average time/residue: 0.3548 time to fit residues: 182.4992 Evaluate side-chains 315 residues out of total 2869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 247 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 686 MET Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 786 CYS Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 920 PHE Chi-restraints excluded: chain A residue 923 GLN Chi-restraints excluded: chain A residue 934 GLN Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 752 CYS Chi-restraints excluded: chain B residue 879 HIS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1034 ASN Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1068 LEU Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 436 HIS Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 495 ASN Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 754 MET Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1076 VAL Chi-restraints excluded: chain C residue 1153 MET Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 261 TYR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 413 PHE Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 848 PHE Chi-restraints excluded: chain D residue 872 THR Chi-restraints excluded: chain D residue 908 THR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1044 ILE Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1065 VAL Chi-restraints excluded: chain D residue 1157 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 10.0000 chunk 294 optimal weight: 0.1980 chunk 84 optimal weight: 0.1980 chunk 254 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 276 optimal weight: 0.7980 chunk 115 optimal weight: 20.0000 chunk 283 optimal weight: 0.7980 chunk 35 optimal weight: 0.0040 chunk 50 optimal weight: 9.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS B 575 GLN ** B 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 924 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 HIS D 333 HIS ** D 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 870 GLN D1081 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.066669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.053352 restraints weight = 218186.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.054776 restraints weight = 142208.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.055741 restraints weight = 103805.840| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 27745 Z= 0.173 Angle : 0.752 17.106 37646 Z= 0.342 Chirality : 0.044 0.200 4153 Planarity : 0.004 0.044 4952 Dihedral : 7.784 141.296 3877 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 2.37 % Allowed : 22.38 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.00 (0.14), residues: 3483 helix: 0.42 (0.14), residues: 1430 sheet: -0.45 (0.25), residues: 457 loop : -1.75 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 838 HIS 0.011 0.001 HIS A 506 PHE 0.047 0.001 PHE D 53 TYR 0.037 0.001 TYR C 706 ARG 0.012 0.001 ARG C 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5611.14 seconds wall clock time: 102 minutes 45.35 seconds (6165.35 seconds total)