Starting phenix.real_space_refine on Tue Feb 20 17:01:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtb_32775/02_2024/7wtb_32775_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtb_32775/02_2024/7wtb_32775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtb_32775/02_2024/7wtb_32775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtb_32775/02_2024/7wtb_32775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtb_32775/02_2024/7wtb_32775_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtb_32775/02_2024/7wtb_32775_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 172 5.16 5 C 18014 2.51 5 N 4957 2.21 5 O 5325 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 47": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 1001": "OE1" <-> "OE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "A GLU 1146": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B GLU 975": "OE1" <-> "OE2" Residue "B GLU 1047": "OE1" <-> "OE2" Residue "B GLU 1049": "OE1" <-> "OE2" Residue "B GLU 1097": "OE1" <-> "OE2" Residue "B GLU 1146": "OE1" <-> "OE2" Residue "C ASP 526": "OD1" <-> "OD2" Residue "C GLU 632": "OE1" <-> "OE2" Residue "C GLU 975": "OE1" <-> "OE2" Residue "C GLU 1000": "OE1" <-> "OE2" Residue "C PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1049": "OE1" <-> "OE2" Residue "C GLU 1051": "OE1" <-> "OE2" Residue "C ASP 1067": "OD1" <-> "OD2" Residue "D GLU 836": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28480 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1146, 8869 Classifications: {'peptide': 1146} Link IDs: {'PTRANS': 65, 'TRANS': 1080} Chain: "B" Number of atoms: 8877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 8877 Classifications: {'peptide': 1147} Link IDs: {'PTRANS': 65, 'TRANS': 1081} Chain: "C" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "D" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5255 Classifications: {'peptide': 684} Link IDs: {'PTRANS': 45, 'TRANS': 638} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'ACO': 1, 'ANP': 1, 'BTI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 97 Unusual residues: {'ACO': 1, 'ANP': 1, 'BTI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.11, per 1000 atoms: 0.50 Number of scatterers: 28480 At special positions: 0 Unit cell: (160.6, 161.7, 137.5, 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 172 16.00 P 12 15.00 O 5325 8.00 N 4957 7.00 C 18014 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=2.04 Simple disulfide: pdb=" SG CYS B 752 " - pdb=" SG CYS B 786 " distance=2.03 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=2.03 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: 11.31 Conformation dependent library (CDL) restraints added in 5.5 seconds 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6738 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 149 helices and 30 sheets defined 39.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.61 Creating SS restraints... Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 211 through 226 removed outlier: 4.234A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 302 Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.313A pdb=" N THR A 334 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A 335 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 Processing helix chain 'A' and resid 357 through 360 No H-bonds generated for 'chain 'A' and resid 357 through 360' Processing helix chain 'A' and resid 436 through 449 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' 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 596 removed outlier: 3.687A 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 617 Processing helix chain 'A' and resid 623 through 633 removed outlier: 3.584A pdb=" N GLU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 633 " --> pdb=" O GLU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 669 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 762 removed outlier: 4.085A pdb=" N ARG A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 799 through 801 No H-bonds generated for 'chain 'A' and resid 799 through 801' Processing helix chain 'A' and resid 810 through 816 Processing helix chain 'A' and resid 828 through 845 removed outlier: 3.696A pdb=" N GLY A 843 " --> pdb=" O GLU A 839 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 844 " --> pdb=" O GLY A 840 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR A 845 " --> pdb=" O ALA A 841 " (cutoff:3.500A) 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 removed outlier: 3.814A pdb=" N TYR A 871 " --> pdb=" O GLY A 868 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR A 872 " --> pdb=" O GLY A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 900 removed outlier: 4.637A pdb=" N LYS A 888 " --> pdb=" O SER A 885 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 891 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 895 " --> pdb=" O LYS A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 928 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 47 through 59 Processing helix chain 'B' and resid 75 through 79 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 143 through 149 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'B' and resid 210 through 227 removed outlier: 3.588A pdb=" N GLU B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 302 Processing helix chain 'B' and resid 331 through 339 removed outlier: 4.013A pdb=" N THR B 334 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 436 through 449 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 485 through 487 No H-bonds generated for 'chain 'B' and resid 485 through 487' Processing helix chain 'B' and resid 496 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 removed outlier: 3.507A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 591 through 597 Processing helix chain 'B' and resid 609 through 617 Processing helix chain 'B' and resid 623 through 631 removed outlier: 3.551A pdb=" N LEU B 630 " --> pdb=" O ARG B 626 " (cutoff:3.500A) 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 Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 799 through 801 No H-bonds generated for 'chain 'B' and resid 799 through 801' Processing helix chain 'B' and resid 810 through 816 Processing helix chain 'B' and resid 828 through 845 removed outlier: 3.763A pdb=" N ASP B 833 " --> pdb=" O GLU B 829 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP B 838 " --> pdb=" O TYR B 834 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR B 845 " --> pdb=" O ALA B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 854 Processing helix chain 'B' and resid 871 through 881 Processing helix chain 'B' and resid 887 through 901 removed outlier: 3.648A pdb=" N LYS B 891 " --> pdb=" O PHE B 887 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR B 894 " --> pdb=" O VAL B 890 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL B 895 " --> pdb=" O LYS B 891 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU B 896 " --> pdb=" O LYS B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 924 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 988 through 998 removed outlier: 3.618A pdb=" N LYS B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) 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 496 through 509 Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 550 through 559 Processing helix chain 'C' and resid 572 through 577 Processing helix chain 'C' and resid 584 through 587 No H-bonds generated for 'chain 'C' and resid 584 through 587' Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 609 through 617 Processing helix chain 'C' and resid 623 through 631 removed outlier: 3.677A pdb=" N LEU C 630 " --> pdb=" O ARG C 626 " (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 removed outlier: 3.697A pdb=" N LEU C 726 " --> pdb=" O TYR C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 759 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 828 through 848 removed outlier: 3.660A pdb=" N ASP C 833 " --> pdb=" O GLU C 829 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU C 844 " --> pdb=" O GLY C 840 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR C 845 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA C 846 " --> pdb=" O ARG C 842 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ALA C 847 " --> pdb=" O GLY C 843 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE C 848 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.633A pdb=" N MET C 854 " --> pdb=" O THR C 851 " (cutoff:3.500A) 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 881 removed outlier: 4.899A pdb=" N THR C 872 " --> pdb=" O GLY C 868 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN C 873 " --> pdb=" O GLY C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 892 removed outlier: 3.667A pdb=" N LYS C 891 " --> pdb=" O PHE C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 Processing helix chain 'C' and resid 912 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 968 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 998 removed outlier: 3.629A pdb=" N LYS C 992 " --> pdb=" O GLN C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1012 Processing helix chain 'C' and resid 1014 through 1027 removed outlier: 3.527A pdb=" N THR C1026 " --> pdb=" O ASP C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1035 through 1040 Processing helix chain 'D' and resid 496 through 510 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 removed outlier: 3.725A pdb=" N ILE D 590 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Proline residue: D 592 - end of helix Processing helix chain 'D' and resid 609 through 617 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 799 through 801 No H-bonds generated for 'chain 'D' and resid 799 through 801' Processing helix chain 'D' and resid 810 through 817 removed outlier: 3.733A pdb=" N THR D 817 " --> pdb=" O LEU D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 828 through 848 removed outlier: 3.711A pdb=" N GLY D 843 " --> pdb=" O GLU D 839 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU D 844 " --> pdb=" O GLY D 840 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR D 845 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA D 846 " --> pdb=" O ARG D 842 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA D 847 " --> pdb=" O GLY D 843 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE D 848 " --> pdb=" O LEU D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 854 removed outlier: 4.093A pdb=" N MET D 854 " --> pdb=" O THR D 851 " (cutoff:3.500A) Processing helix chain 'D' and resid 860 through 864 Processing helix chain 'D' and resid 868 through 880 removed outlier: 4.727A pdb=" N THR D 872 " --> pdb=" O GLY D 868 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN D 873 " --> pdb=" O GLY D 869 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 900 removed outlier: 5.031A pdb=" N LYS D 888 " --> pdb=" O SER D 885 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 891 " --> pdb=" O LYS D 888 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL D 895 " --> pdb=" O LYS D 892 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET D 900 " --> pdb=" O ALA D 897 " (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 989 through 997 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 137 through 139 removed outlier: 6.441A pdb=" N ARG A 62 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL A 42 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL A 64 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU A 82 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR A 67 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR A 84 " --> pdb=" O TYR A 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 191 through 195 removed outlier: 3.801A pdb=" N ILE A 192 " --> pdb=" O GLU A 236 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 236 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 262 through 264 removed outlier: 3.757A pdb=" N GLU A 324 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 249 through 251 Processing sheet with id= E, first strand: chain 'A' and resid 275 through 277 Processing sheet with id= F, first strand: chain 'A' and resid 396 through 398 Processing sheet with id= G, first strand: chain 'A' and resid 564 through 567 Processing sheet with id= H, first strand: chain 'A' and resid 640 through 644 removed outlier: 7.037A pdb=" N VAL A 673 " --> pdb=" O MET A 641 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 643 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG A 675 " --> pdb=" O LEU A 643 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 699 " --> pdb=" O PHE A 674 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL A 676 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU A 701 " --> pdb=" O VAL A 676 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 737 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE A 704 " --> pdb=" O ILE A 737 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N CYS A 739 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ILE A 740 " --> pdb=" O PRO A 767 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS A 769 " --> pdb=" O ILE A 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 1047 through 1051 removed outlier: 7.002A pdb=" N PHE A1077 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N VAL A1065 " --> pdb=" O GLN A1075 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN A1075 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1119 through 1123 removed outlier: 7.004A pdb=" N VAL A1139 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE A1123 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LEU A1137 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A1149 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL A1139 " --> pdb=" O THR A1147 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR A1147 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 137 through 139 removed outlier: 6.694A pdb=" N ARG B 62 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL B 42 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 64 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N GLU B 82 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR B 67 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR B 84 " --> pdb=" O TYR B 67 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 204 through 207 Processing sheet with id= M, first strand: chain 'B' and resid 262 through 264 removed outlier: 3.602A pdb=" N ILE B 245 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 324 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU B 313 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 249 through 251 Processing sheet with id= O, first strand: chain 'B' and resid 275 through 277 removed outlier: 4.047A pdb=" N VAL B 427 " --> pdb=" O VAL B 378 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 396 through 398 removed outlier: 4.284A pdb=" N VAL B 396 " --> pdb=" O ARG B 453 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 453 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 398 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG B 451 " --> pdb=" O ARG B 398 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'B' and resid 564 through 567 Processing sheet with id= R, first strand: chain 'B' and resid 767 through 772 removed outlier: 6.781A pdb=" N MET B 604 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU B 642 " --> pdb=" O MET B 604 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASN B 606 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 12.689A pdb=" N ARG B 644 " --> pdb=" O ASN B 606 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 1047 through 1051 removed outlier: 7.008A pdb=" N PHE B1077 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B1065 " --> pdb=" O GLN B1075 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN B1075 " --> pdb=" O VAL B1065 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1136 through 1141 removed outlier: 6.690A pdb=" N VAL B1149 " --> pdb=" O LEU B1137 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B1139 " --> pdb=" O THR B1147 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR B1147 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 564 through 567 Processing sheet with id= V, first strand: chain 'C' and resid 640 through 644 removed outlier: 7.239A pdb=" N VAL C 673 " --> pdb=" O MET C 641 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU C 643 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG C 675 " --> pdb=" O LEU C 643 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL C 699 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL C 676 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU C 701 " --> pdb=" O VAL C 676 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 737 " --> pdb=" O ALA C 702 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE C 704 " --> pdb=" O ILE C 737 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N CYS C 739 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE C 740 " --> pdb=" O PRO C 767 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N HIS C 769 " --> pdb=" O ILE C 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'C' and resid 1047 through 1049 removed outlier: 6.857A pdb=" N PHE C1077 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL C1065 " --> pdb=" O GLN C1075 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN C1075 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 1136 through 1141 removed outlier: 6.706A pdb=" N VAL C1149 " --> pdb=" O LEU C1137 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL C1139 " --> pdb=" O THR C1147 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N THR C1147 " --> pdb=" O VAL C1139 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 1157 through 1160 removed outlier: 6.944A pdb=" N GLU C1176 " --> pdb=" O ARG C1158 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 564 through 567 Processing sheet with id= AA, first strand: chain 'D' and resid 768 through 771 removed outlier: 6.805A pdb=" N LEU D 738 " --> pdb=" O HIS D 769 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N HIS D 771 " --> pdb=" O LEU D 738 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE D 740 " --> pdb=" O HIS D 771 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET D 604 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU D 642 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ASN D 606 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 13.114A pdb=" N ARG D 644 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.854A pdb=" N PHE D1077 " --> pdb=" O LEU D1063 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'D' and resid 1129 through 1131 removed outlier: 3.775A pdb=" N ALA D1129 " --> pdb=" O VAL D1157 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 1119 through 1123 removed outlier: 7.074A pdb=" N VAL D1139 " --> pdb=" O ILE D1121 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE D1123 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU D1137 " --> pdb=" O ILE D1123 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL D1149 " --> pdb=" O LEU D1137 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL D1139 " --> pdb=" O THR D1147 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR D1147 " --> pdb=" O VAL D1139 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2721 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: 11.77 Time building geometry restraints manager: 12.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4817 1.31 - 1.43: 7272 1.43 - 1.56: 16671 1.56 - 1.69: 50 1.69 - 1.82: 300 Bond restraints: 29110 Sorted by residual: bond pdb=" C6 BTI C1900 " pdb=" S1 BTI C1900 " ideal model delta sigma weight residual 1.811 1.442 0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C6 BTI D1900 " pdb=" S1 BTI D1900 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI B2002 " pdb=" S1 BTI B2002 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C6 BTI A1201 " pdb=" S1 BTI A1201 " ideal model delta sigma weight residual 1.811 1.443 0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C2' ANP A1202 " pdb=" C3' ANP A1202 " ideal model delta sigma weight residual 1.520 1.225 0.295 2.00e-02 2.50e+03 2.17e+02 ... (remaining 29105 not shown) Histogram of bond angle deviations from ideal: 91.06 - 103.22: 398 103.22 - 115.38: 18359 115.38 - 127.54: 20437 127.54 - 139.70: 283 139.70 - 151.86: 2 Bond angle restraints: 39479 Sorted by residual: angle pdb=" C10 BTI B2002 " pdb=" C11 BTI B2002 " pdb=" O11 BTI B2002 " ideal model delta sigma weight residual 125.49 91.06 34.43 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C10 BTI C1900 " pdb=" C11 BTI C1900 " pdb=" O11 BTI C1900 " ideal model delta sigma weight residual 125.49 93.15 32.34 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C1' ANP A1202 " pdb=" N9 ANP A1202 " pdb=" C8 ANP A1202 " ideal model delta sigma weight residual 128.35 98.16 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C1' ANP B2003 " pdb=" N9 ANP B2003 " pdb=" C8 ANP B2003 " ideal model delta sigma weight residual 128.35 98.48 29.87 3.00e+00 1.11e-01 9.91e+01 angle pdb=" C10 BTI A1201 " pdb=" C11 BTI A1201 " pdb=" O11 BTI A1201 " ideal model delta sigma weight residual 125.49 97.93 27.56 3.00e+00 1.11e-01 8.44e+01 ... (remaining 39474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.19: 15986 18.19 - 36.37: 1365 36.37 - 54.56: 274 54.56 - 72.75: 96 72.75 - 90.93: 34 Dihedral angle restraints: 17755 sinusoidal: 7258 harmonic: 10497 Sorted by residual: 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 93.00 179.42 -86.42 1 1.00e+01 1.00e-02 9.00e+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 93.00 173.64 -80.64 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS D 752 " pdb=" SG CYS D 752 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual 93.00 154.11 -61.11 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 17752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3945 0.084 - 0.168: 401 0.168 - 0.251: 35 0.251 - 0.335: 1 0.335 - 0.419: 4 Chirality restraints: 4386 Sorted by residual: chirality pdb=" CA ARG C1036 " pdb=" N ARG C1036 " pdb=" C ARG C1036 " pdb=" CB ARG C1036 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CA THR C1035 " pdb=" N THR C1035 " pdb=" C THR C1035 " pdb=" CB THR C1035 " both_signs ideal model delta sigma weight residual False 2.53 2.92 -0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2' ANP B2003 " pdb=" C1' ANP B2003 " pdb=" C3' ANP B2003 " pdb=" O2' ANP B2003 " both_signs ideal model delta sigma weight residual False -2.72 -2.35 -0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 4383 not shown) Planarity restraints: 5173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 511 " 0.033 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" C GLY D 511 " -0.114 2.00e-02 2.50e+03 pdb=" O GLY D 511 " 0.040 2.00e-02 2.50e+03 pdb=" N PRO D 512 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 508 " 0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C MET D 508 " -0.087 2.00e-02 2.50e+03 pdb=" O MET D 508 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL D 509 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C1038 " 0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C PHE C1038 " -0.086 2.00e-02 2.50e+03 pdb=" O PHE C1038 " 0.032 2.00e-02 2.50e+03 pdb=" N LEU C1039 " 0.030 2.00e-02 2.50e+03 ... (remaining 5170 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 484 2.67 - 3.23: 27296 3.23 - 3.78: 44362 3.78 - 4.34: 57013 4.34 - 4.90: 93988 Nonbonded interactions: 223143 Sorted by model distance: nonbonded pdb=" C8 ANP B2003 " pdb=" O4' ANP B2003 " model vdw 2.109 2.608 nonbonded pdb=" O ALA C1132 " pdb=" OG SER C1151 " model vdw 2.125 2.440 nonbonded pdb=" O THR B1156 " pdb=" NH1 ARG B1158 " model vdw 2.190 2.520 nonbonded pdb=" ND2 ASN B 44 " pdb=" O PRO B 116 " model vdw 2.192 2.520 nonbonded pdb=" OD1 ASN A1069 " pdb=" N ARG A1070 " model vdw 2.192 2.520 ... (remaining 223138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 1178) selection = (chain 'B' and resid 33 through 1178) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 2.160 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: 7.060 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 76.370 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.008 0.369 29110 Z= 0.573 Angle : 0.918 34.430 39479 Z= 0.490 Chirality : 0.049 0.419 4386 Planarity : 0.005 0.076 5173 Dihedral : 14.936 90.932 11005 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.90 % Favored : 92.88 % Rotamer: Outliers : 1.76 % Allowed : 0.73 % Favored : 97.51 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3653 helix: 1.66 (0.14), residues: 1444 sheet: 0.15 (0.23), residues: 533 loop : -1.47 (0.14), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 607 HIS 0.010 0.001 HIS A 271 PHE 0.023 0.001 PHE A 387 TYR 0.017 0.001 TYR A 261 ARG 0.013 0.001 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 552 time to evaluate : 3.278 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: 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 75 MET cc_start: 0.8050 (mtm) cc_final: 0.7718 (mtm) REVERT: A 783 MET cc_start: 0.8721 (mmt) cc_final: 0.8387 (mmp) REVERT: A 1098 MET cc_start: 0.3768 (tmm) cc_final: 0.2484 (tpt) REVERT: B 149 MET cc_start: 0.6869 (mmp) cc_final: 0.6586 (tmm) REVERT: B 395 GLU cc_start: 0.7426 (mp0) cc_final: 0.7202 (mp0) REVERT: B 428 LYS cc_start: 0.8555 (mtmt) cc_final: 0.7824 (tttt) REVERT: B 471 PHE cc_start: 0.8640 (t80) cc_final: 0.8417 (t80) REVERT: B 743 MET cc_start: 0.8468 (pmm) cc_final: 0.8213 (pmm) REVERT: B 836 GLU cc_start: 0.8836 (tp30) cc_final: 0.8542 (tp30) REVERT: B 1006 ASP cc_start: 0.9221 (m-30) cc_final: 0.9009 (m-30) REVERT: C 519 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7481 (mmmt) REVERT: C 584 THR cc_start: 0.8741 (m) cc_final: 0.8516 (p) REVERT: C 671 MET cc_start: 0.4761 (tpt) cc_final: 0.4392 (tpp) REVERT: C 739 CYS cc_start: 0.7302 (t) cc_final: 0.7040 (t) REVERT: C 1012 MET cc_start: 0.8271 (mmm) cc_final: 0.8045 (mmt) REVERT: C 1038 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7332 (p90) REVERT: C 1048 PHE cc_start: 0.5958 (OUTLIER) cc_final: 0.5204 (p90) REVERT: C 1164 LYS cc_start: 0.8506 (tmtt) cc_final: 0.8304 (tptp) REVERT: C 1165 ASP cc_start: 0.8489 (m-30) cc_final: 0.8109 (m-30) REVERT: D 566 MET cc_start: 0.6876 (ttp) cc_final: 0.6267 (ptm) REVERT: D 873 ASN cc_start: 0.7998 (m110) cc_final: 0.7747 (m-40) REVERT: D 1153 MET cc_start: 0.7279 (ptt) cc_final: 0.6816 (pmm) REVERT: D 1171 ASP cc_start: 0.8938 (m-30) cc_final: 0.8258 (m-30) outliers start: 53 outliers final: 9 residues processed: 592 average time/residue: 0.4530 time to fit residues: 405.7686 Evaluate side-chains 325 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 313 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1053 GLU Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain D residue 496 ARG Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1056 LYS Chi-restraints excluded: chain D residue 1059 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 1.9990 chunk 275 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 186 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 330 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 924 ASN A 988 GLN A1135 GLN B 94 GLN B 306 ASN B 348 GLN B 375 GLN B 479 GLN B 681 ASN ** B 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 873 ASN ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 807 GLN C 873 ASN C 923 GLN C1059 HIS ** C1075 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** D 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29110 Z= 0.221 Angle : 0.648 9.312 39479 Z= 0.326 Chirality : 0.044 0.287 4386 Planarity : 0.005 0.076 5173 Dihedral : 8.677 66.840 4242 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.29 % Rotamer: Outliers : 2.26 % Allowed : 11.22 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3653 helix: 1.58 (0.14), residues: 1457 sheet: 0.18 (0.23), residues: 523 loop : -1.49 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 838 HIS 0.010 0.001 HIS C 502 PHE 0.037 0.001 PHE A1100 TYR 0.015 0.001 TYR B 261 ARG 0.007 0.001 ARG C 625 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 325 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8111 (mtm) cc_final: 0.7821 (mtm) REVERT: A 403 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7104 (mmp) REVERT: A 1054 ARG cc_start: 0.7445 (ptt90) cc_final: 0.7211 (ptt90) REVERT: B 41 MET cc_start: 0.5780 (ttp) cc_final: 0.5289 (tmm) REVERT: B 288 ARG cc_start: 0.8625 (mtt90) cc_final: 0.8394 (mmt90) REVERT: B 377 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6666 (mtm180) REVERT: B 428 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8130 (tttt) REVERT: B 743 MET cc_start: 0.8518 (pmm) cc_final: 0.8178 (pmm) REVERT: B 783 MET cc_start: 0.8896 (mmt) cc_final: 0.8695 (tpp) REVERT: B 994 LEU cc_start: 0.9360 (mt) cc_final: 0.8966 (pp) REVERT: B 1006 ASP cc_start: 0.9326 (m-30) cc_final: 0.9058 (m-30) REVERT: B 1101 HIS cc_start: 0.7843 (m-70) cc_final: 0.7607 (m-70) REVERT: B 1116 MET cc_start: 0.8446 (ttt) cc_final: 0.8245 (ttt) REVERT: C 801 MET cc_start: 0.8008 (mpp) cc_final: 0.7746 (mtt) REVERT: C 1038 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7486 (p90) REVERT: C 1048 PHE cc_start: 0.5825 (OUTLIER) cc_final: 0.5370 (p90) REVERT: D 566 MET cc_start: 0.6809 (ttp) cc_final: 0.6243 (ptm) REVERT: D 683 LEU cc_start: 0.8885 (mp) cc_final: 0.8291 (mm) REVERT: D 783 MET cc_start: 0.8942 (mmt) cc_final: 0.8644 (mmp) REVERT: D 873 ASN cc_start: 0.7897 (m110) cc_final: 0.7685 (m-40) REVERT: D 1143 MET cc_start: -0.1800 (ttp) cc_final: -0.2780 (ttp) REVERT: D 1153 MET cc_start: 0.7447 (ptt) cc_final: 0.6867 (pmm) outliers start: 68 outliers final: 42 residues processed: 373 average time/residue: 0.4565 time to fit residues: 266.9404 Evaluate side-chains 311 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 266 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain C residue 521 SER Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 813 LEU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 896 GLU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1059 HIS Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 331 optimal weight: 0.6980 chunk 357 optimal weight: 4.9990 chunk 294 optimal weight: 4.9990 chunk 328 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 484 ASN A1073 GLN ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS B 769 HIS B 877 GLN B 956 HIS C 506 HIS ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 769 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 873 ASN C 879 HIS D 681 ASN D 864 ASN ** D1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29110 Z= 0.302 Angle : 0.673 13.959 39479 Z= 0.341 Chirality : 0.044 0.199 4386 Planarity : 0.005 0.056 5173 Dihedral : 7.535 68.002 4225 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.14 % Favored : 92.75 % Rotamer: Outliers : 3.68 % Allowed : 12.91 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3653 helix: 1.32 (0.14), residues: 1472 sheet: -0.04 (0.22), residues: 551 loop : -1.54 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 624 HIS 0.008 0.001 HIS C1059 PHE 0.026 0.002 PHE B 674 TYR 0.023 0.002 TYR C 593 ARG 0.023 0.001 ARG C 997 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 282 time to evaluate : 2.919 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 75 MET cc_start: 0.8439 (mtm) cc_final: 0.8152 (mtm) REVERT: A 275 VAL cc_start: 0.8733 (t) cc_final: 0.8510 (p) REVERT: A 403 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7504 (mmp) REVERT: A 501 LEU cc_start: 0.9642 (mm) cc_final: 0.9405 (mm) REVERT: A 508 MET cc_start: 0.8807 (mmp) cc_final: 0.8416 (mmm) REVERT: A 607 TRP cc_start: 0.7840 (OUTLIER) cc_final: 0.7003 (t60) REVERT: A 801 MET cc_start: 0.8952 (mtp) cc_final: 0.8708 (mtm) REVERT: A 822 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8665 (pp) REVERT: A 1031 ASP cc_start: 0.6328 (t0) cc_final: 0.6127 (t70) REVERT: A 1101 HIS cc_start: 0.7987 (m-70) cc_final: 0.7742 (m-70) REVERT: B 41 MET cc_start: 0.6368 (ttp) cc_final: 0.5417 (tmm) REVERT: B 42 VAL cc_start: 0.8426 (OUTLIER) cc_final: 0.7983 (m) REVERT: B 149 MET cc_start: 0.7970 (tmm) cc_final: 0.7580 (mmp) REVERT: B 377 ARG cc_start: 0.7227 (mtm-85) cc_final: 0.6904 (mtm180) REVERT: B 428 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8481 (mttt) REVERT: B 743 MET cc_start: 0.8697 (pmm) cc_final: 0.8347 (pmm) REVERT: B 836 GLU cc_start: 0.8935 (tp30) cc_final: 0.8719 (tp30) REVERT: B 854 MET cc_start: 0.6771 (tpt) cc_final: 0.6162 (tpt) REVERT: B 921 MET cc_start: 0.8971 (mtp) cc_final: 0.8757 (mtp) REVERT: B 994 LEU cc_start: 0.9402 (mt) cc_final: 0.9111 (pp) REVERT: B 1006 ASP cc_start: 0.9321 (m-30) cc_final: 0.8962 (m-30) REVERT: B 1098 MET cc_start: 0.1133 (OUTLIER) cc_final: 0.0600 (tmm) REVERT: B 1145 MET cc_start: 0.6831 (pmm) cc_final: 0.4961 (ptp) REVERT: C 604 MET cc_start: 0.8313 (tmm) cc_final: 0.8033 (tmm) REVERT: C 1038 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8103 (p90) REVERT: C 1059 HIS cc_start: 0.8582 (m90) cc_final: 0.8339 (m-70) REVERT: D 566 MET cc_start: 0.6858 (ttp) cc_final: 0.6179 (ptm) REVERT: D 625 ARG cc_start: 0.8362 (mmt180) cc_final: 0.7953 (mmm160) REVERT: D 683 LEU cc_start: 0.8933 (mp) cc_final: 0.8731 (mm) REVERT: D 724 MET cc_start: 0.8480 (mmm) cc_final: 0.8279 (mmm) REVERT: D 743 MET cc_start: 0.8535 (pmm) cc_final: 0.8174 (pmm) REVERT: D 783 MET cc_start: 0.9117 (mmt) cc_final: 0.8580 (mmm) REVERT: D 881 MET cc_start: 0.8226 (mmt) cc_final: 0.7931 (tpp) REVERT: D 1054 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5891 (mpp-170) REVERT: D 1067 ASP cc_start: 0.6216 (p0) cc_final: 0.5832 (p0) REVERT: D 1143 MET cc_start: -0.1316 (ttp) cc_final: -0.1719 (ttp) REVERT: D 1153 MET cc_start: 0.7705 (ptt) cc_final: 0.7194 (pmm) outliers start: 111 outliers final: 76 residues processed: 363 average time/residue: 0.4040 time to fit residues: 232.1557 Evaluate side-chains 335 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 252 time to evaluate : 3.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 656 ASP Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1086 SER Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 687 LEU Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 833 ASP Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1163 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 36 optimal weight: 0.0980 chunk 158 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 332 optimal weight: 0.0040 chunk 351 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 overall best weight: 2.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 HIS A 653 ASN A1135 GLN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN B 877 GLN C 769 HIS ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1081 ASN ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29110 Z= 0.248 Angle : 0.608 9.561 39479 Z= 0.307 Chirality : 0.042 0.217 4386 Planarity : 0.004 0.046 5173 Dihedral : 7.157 72.777 4221 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.01 % Favored : 92.91 % Rotamer: Outliers : 3.42 % Allowed : 15.50 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.14), residues: 3653 helix: 1.42 (0.14), residues: 1471 sheet: 0.07 (0.23), residues: 547 loop : -1.52 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 607 HIS 0.017 0.001 HIS D1059 PHE 0.017 0.001 PHE B 461 TYR 0.017 0.002 TYR A 118 ARG 0.007 0.000 ARG C 715 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 259 time to evaluate : 3.243 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 75 MET cc_start: 0.8535 (mtm) cc_final: 0.8217 (mtm) REVERT: A 501 LEU cc_start: 0.9648 (mm) cc_final: 0.9411 (mm) REVERT: A 508 MET cc_start: 0.8716 (mmp) cc_final: 0.8277 (mmm) REVERT: A 607 TRP cc_start: 0.7814 (OUTLIER) cc_final: 0.6877 (t60) REVERT: A 822 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8599 (pp) REVERT: B 41 MET cc_start: 0.6705 (ttp) cc_final: 0.5823 (tmm) REVERT: B 377 ARG cc_start: 0.7003 (mtm-85) cc_final: 0.6783 (mtm180) REVERT: B 651 TYR cc_start: 0.7628 (m-80) cc_final: 0.7070 (m-10) REVERT: B 743 MET cc_start: 0.8709 (pmm) cc_final: 0.8352 (pmm) REVERT: B 801 MET cc_start: 0.9000 (mtt) cc_final: 0.8705 (mtm) REVERT: B 836 GLU cc_start: 0.8895 (tp30) cc_final: 0.8661 (tp30) REVERT: B 921 MET cc_start: 0.8942 (mtp) cc_final: 0.8713 (mpp) REVERT: B 994 LEU cc_start: 0.9357 (mt) cc_final: 0.9078 (pp) REVERT: B 1006 ASP cc_start: 0.9335 (m-30) cc_final: 0.8981 (m-30) REVERT: B 1098 MET cc_start: 0.0493 (OUTLIER) cc_final: -0.0067 (tmm) REVERT: B 1116 MET cc_start: 0.8786 (ttt) cc_final: 0.8508 (ttt) REVERT: B 1166 MET cc_start: 0.8977 (tpt) cc_final: 0.8707 (ppp) REVERT: C 566 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8279 (ptm) REVERT: C 604 MET cc_start: 0.8202 (tmm) cc_final: 0.7798 (tmm) REVERT: C 801 MET cc_start: 0.8718 (tpp) cc_final: 0.8376 (mtt) REVERT: C 804 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8386 (mmt) REVERT: C 881 MET cc_start: 0.8862 (mmp) cc_final: 0.8636 (tpp) REVERT: C 1038 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8381 (p90) REVERT: D 566 MET cc_start: 0.6879 (ttp) cc_final: 0.6108 (ptm) REVERT: D 625 ARG cc_start: 0.8177 (mmt180) cc_final: 0.7882 (mmm160) REVERT: D 783 MET cc_start: 0.9197 (mmt) cc_final: 0.8623 (mmm) REVERT: D 1078 PHE cc_start: 0.8442 (m-10) cc_final: 0.8227 (m-80) REVERT: D 1143 MET cc_start: -0.1750 (ttp) cc_final: -0.2569 (ttp) REVERT: D 1153 MET cc_start: 0.7666 (ptt) cc_final: 0.7132 (pmm) outliers start: 103 outliers final: 71 residues processed: 333 average time/residue: 0.4121 time to fit residues: 217.4202 Evaluate side-chains 314 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 237 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 970 ASP Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 376 CYS Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 557 VAL Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 804 MET Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1165 ASP Chi-restraints excluded: chain C residue 1168 LEU Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 526 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1163 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 261 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 300 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29110 Z= 0.177 Angle : 0.578 9.437 39479 Z= 0.286 Chirality : 0.042 0.229 4386 Planarity : 0.004 0.054 5173 Dihedral : 6.921 73.049 4221 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.65 % Favored : 93.24 % Rotamer: Outliers : 3.42 % Allowed : 15.86 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3653 helix: 1.55 (0.14), residues: 1460 sheet: 0.10 (0.23), residues: 547 loop : -1.48 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 607 HIS 0.015 0.001 HIS D1059 PHE 0.018 0.001 PHE B 674 TYR 0.019 0.001 TYR B 651 ARG 0.010 0.000 ARG B 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 257 time to evaluate : 3.161 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: A 75 MET cc_start: 0.8525 (mtm) cc_final: 0.8172 (mtm) REVERT: A 276 GLU cc_start: 0.7376 (mp0) cc_final: 0.7136 (mp0) REVERT: A 375 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7757 (tm-30) REVERT: A 401 GLU cc_start: 0.8387 (pm20) cc_final: 0.8148 (pm20) REVERT: A 501 LEU cc_start: 0.9643 (mm) cc_final: 0.9433 (mm) REVERT: A 508 MET cc_start: 0.8651 (mmp) cc_final: 0.8355 (mmm) REVERT: A 607 TRP cc_start: 0.7721 (OUTLIER) cc_final: 0.6711 (t60) REVERT: A 616 MET cc_start: 0.7638 (mmp) cc_final: 0.7394 (mmp) REVERT: A 822 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8589 (pp) REVERT: A 921 MET cc_start: 0.9014 (ttp) cc_final: 0.8769 (mtp) REVERT: B 41 MET cc_start: 0.6835 (ttp) cc_final: 0.4986 (tmm) REVERT: B 47 GLU cc_start: 0.7974 (pm20) cc_final: 0.7209 (pm20) REVERT: B 377 ARG cc_start: 0.6959 (mtm-85) cc_final: 0.6682 (mtm180) REVERT: B 379 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8569 (t) REVERT: B 428 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8432 (mttt) REVERT: B 743 MET cc_start: 0.8676 (pmm) cc_final: 0.8327 (pmm) REVERT: B 801 MET cc_start: 0.8963 (mtt) cc_final: 0.8607 (mtm) REVERT: B 804 MET cc_start: 0.8284 (mmm) cc_final: 0.7936 (mmm) REVERT: B 836 GLU cc_start: 0.8899 (tp30) cc_final: 0.8637 (tp30) REVERT: B 854 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5691 (tpt) REVERT: B 921 MET cc_start: 0.8919 (mtp) cc_final: 0.8712 (mpp) REVERT: B 994 LEU cc_start: 0.9427 (mt) cc_final: 0.9118 (pp) REVERT: B 1006 ASP cc_start: 0.9331 (m-30) cc_final: 0.8908 (m-30) REVERT: B 1097 GLU cc_start: 0.2196 (OUTLIER) cc_final: 0.1992 (pm20) REVERT: B 1116 MET cc_start: 0.8815 (ttt) cc_final: 0.8555 (ttt) REVERT: C 566 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8229 (ptm) REVERT: C 604 MET cc_start: 0.8249 (tmm) cc_final: 0.7813 (tmm) REVERT: C 616 MET cc_start: 0.8609 (mmm) cc_final: 0.8106 (mmp) REVERT: C 801 MET cc_start: 0.8706 (tpp) cc_final: 0.8375 (mtt) REVERT: C 881 MET cc_start: 0.8883 (mmp) cc_final: 0.8661 (tpp) REVERT: D 566 MET cc_start: 0.6849 (ttp) cc_final: 0.5953 (ptm) REVERT: D 625 ARG cc_start: 0.8167 (mmt180) cc_final: 0.7876 (mmm160) REVERT: D 724 MET cc_start: 0.8578 (mmm) cc_final: 0.8276 (mmm) REVERT: D 755 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8502 (mm) REVERT: D 783 MET cc_start: 0.9184 (mmt) cc_final: 0.8958 (mmm) REVERT: D 810 MET cc_start: 0.8908 (mmm) cc_final: 0.8580 (mmm) REVERT: D 886 LYS cc_start: 0.9321 (mmmt) cc_final: 0.9046 (mttp) REVERT: D 1143 MET cc_start: -0.1610 (ttp) cc_final: -0.2276 (ttp) REVERT: D 1153 MET cc_start: 0.7780 (ptt) cc_final: 0.7293 (pmm) outliers start: 103 outliers final: 73 residues processed: 334 average time/residue: 0.3992 time to fit residues: 212.7787 Evaluate side-chains 317 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 236 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 970 ASP Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 944 VAL Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 647 ASN Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1052 LEU Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1086 SER Chi-restraints excluded: chain D residue 1163 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 6.9990 chunk 316 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 206 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 292 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 chunk 116 optimal weight: 0.1980 chunk 184 optimal weight: 2.9990 overall best weight: 0.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 HIS A1135 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 807 GLN B 873 ASN ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 574 HIS ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 29110 Z= 0.152 Angle : 0.578 9.681 39479 Z= 0.283 Chirality : 0.042 0.240 4386 Planarity : 0.004 0.047 5173 Dihedral : 6.666 80.733 4221 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.35 % Favored : 93.54 % Rotamer: Outliers : 2.72 % Allowed : 17.03 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3653 helix: 1.59 (0.14), residues: 1449 sheet: 0.16 (0.23), residues: 527 loop : -1.41 (0.14), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 607 HIS 0.012 0.001 HIS D1059 PHE 0.015 0.001 PHE B 471 TYR 0.013 0.001 TYR B 261 ARG 0.009 0.000 ARG D 715 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 264 time to evaluate : 3.285 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 75 MET cc_start: 0.8548 (mtm) cc_final: 0.8193 (mtm) REVERT: A 276 GLU cc_start: 0.7502 (mp0) cc_final: 0.7028 (mp0) REVERT: A 375 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: A 401 GLU cc_start: 0.8461 (pm20) cc_final: 0.8054 (pm20) REVERT: A 501 LEU cc_start: 0.9639 (mm) cc_final: 0.9420 (mm) REVERT: A 822 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8584 (pp) REVERT: B 41 MET cc_start: 0.6786 (ttp) cc_final: 0.4849 (tmm) REVERT: B 47 GLU cc_start: 0.7985 (pm20) cc_final: 0.7122 (pm20) REVERT: B 377 ARG cc_start: 0.7009 (mtm-85) cc_final: 0.6734 (mtm180) REVERT: B 379 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8605 (t) REVERT: B 428 LYS cc_start: 0.8867 (mtmt) cc_final: 0.8574 (mtmt) REVERT: B 671 MET cc_start: 0.6426 (tpt) cc_final: 0.5497 (tpt) REVERT: B 743 MET cc_start: 0.8674 (pmm) cc_final: 0.8335 (pmm) REVERT: B 801 MET cc_start: 0.8924 (mtt) cc_final: 0.8518 (mtt) REVERT: B 854 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.5627 (tpt) REVERT: B 921 MET cc_start: 0.8990 (mtp) cc_final: 0.8740 (mpp) REVERT: B 994 LEU cc_start: 0.9381 (mt) cc_final: 0.9020 (pp) REVERT: B 1006 ASP cc_start: 0.9339 (m-30) cc_final: 0.8864 (m-30) REVERT: B 1097 GLU cc_start: 0.1985 (OUTLIER) cc_final: 0.1540 (pm20) REVERT: C 566 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8326 (ptm) REVERT: C 616 MET cc_start: 0.8520 (mmm) cc_final: 0.8065 (mmp) REVERT: C 619 LEU cc_start: 0.9103 (mm) cc_final: 0.8900 (mp) REVERT: C 881 MET cc_start: 0.8920 (mmp) cc_final: 0.8660 (tpp) REVERT: C 1036 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7875 (tmm-80) REVERT: D 566 MET cc_start: 0.6851 (ttp) cc_final: 0.6074 (ptm) REVERT: D 625 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7837 (mmm160) REVERT: D 724 MET cc_start: 0.8652 (mmm) cc_final: 0.8249 (mmm) REVERT: D 754 MET cc_start: 0.9156 (tmm) cc_final: 0.8857 (tmm) REVERT: D 783 MET cc_start: 0.9001 (mmt) cc_final: 0.8754 (mmm) REVERT: D 810 MET cc_start: 0.8791 (mmm) cc_final: 0.8534 (mmm) REVERT: D 1143 MET cc_start: -0.1886 (ttp) cc_final: -0.2511 (ttp) REVERT: D 1153 MET cc_start: 0.7796 (ptt) cc_final: 0.7358 (pmm) outliers start: 82 outliers final: 53 residues processed: 326 average time/residue: 0.3948 time to fit residues: 206.2199 Evaluate side-chains 302 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 243 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1123 ILE Chi-restraints excluded: chain A residue 1135 GLN Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 854 MET Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1157 VAL Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 1084 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 257 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 350 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 213 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 ASN A 879 HIS A1093 GLN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 ASN B 873 ASN ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 HIS ** D 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 29110 Z= 0.265 Angle : 0.618 10.881 39479 Z= 0.308 Chirality : 0.042 0.322 4386 Planarity : 0.004 0.050 5173 Dihedral : 6.620 78.848 4219 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.14 % Favored : 92.77 % Rotamer: Outliers : 3.35 % Allowed : 17.19 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3653 helix: 1.51 (0.14), residues: 1467 sheet: 0.00 (0.22), residues: 561 loop : -1.39 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 607 HIS 0.009 0.001 HIS C 998 PHE 0.016 0.001 PHE B 234 TYR 0.017 0.001 TYR A 118 ARG 0.012 0.000 ARG B1070 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 240 time to evaluate : 3.342 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: A 75 MET cc_start: 0.8676 (mtm) cc_final: 0.8327 (mtm) REVERT: A 149 MET cc_start: 0.8955 (mmp) cc_final: 0.8723 (mmt) REVERT: A 276 GLU cc_start: 0.7343 (mp0) cc_final: 0.6897 (mp0) REVERT: A 375 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: A 401 GLU cc_start: 0.8514 (pm20) cc_final: 0.8098 (pm20) REVERT: A 501 LEU cc_start: 0.9676 (mm) cc_final: 0.9463 (mm) REVERT: A 508 MET cc_start: 0.8833 (mmm) cc_final: 0.8408 (mmm) REVERT: A 783 MET cc_start: 0.8848 (tpp) cc_final: 0.8551 (tpp) REVERT: A 822 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8572 (pp) REVERT: A 854 MET cc_start: 0.7402 (mmt) cc_final: 0.6963 (mmt) REVERT: B 41 MET cc_start: 0.7131 (ttp) cc_final: 0.6619 (tmm) REVERT: B 47 GLU cc_start: 0.8063 (pm20) cc_final: 0.6978 (pm20) REVERT: B 377 ARG cc_start: 0.7088 (mtm-85) cc_final: 0.6832 (mtm180) REVERT: B 379 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8663 (t) REVERT: B 428 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8588 (mtmt) REVERT: B 743 MET cc_start: 0.8720 (pmm) cc_final: 0.8406 (pmm) REVERT: B 801 MET cc_start: 0.9001 (mtt) cc_final: 0.8622 (mtm) REVERT: B 836 GLU cc_start: 0.8910 (tp30) cc_final: 0.8576 (tp30) REVERT: B 839 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8513 (tm-30) REVERT: B 921 MET cc_start: 0.9018 (mtp) cc_final: 0.8815 (mtp) REVERT: B 994 LEU cc_start: 0.9421 (mt) cc_final: 0.9115 (pp) REVERT: B 1006 ASP cc_start: 0.9351 (m-30) cc_final: 0.8942 (m-30) REVERT: B 1097 GLU cc_start: 0.2106 (OUTLIER) cc_final: 0.1782 (pm20) REVERT: B 1145 MET cc_start: 0.6940 (pmm) cc_final: 0.5625 (ptm) REVERT: B 1165 ASP cc_start: 0.9000 (t0) cc_final: 0.8574 (m-30) REVERT: C 566 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8304 (ptm) REVERT: C 616 MET cc_start: 0.8680 (mmm) cc_final: 0.8245 (mmp) REVERT: C 854 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6213 (tmm) REVERT: C 1036 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7938 (ptm-80) REVERT: C 1048 PHE cc_start: 0.5922 (OUTLIER) cc_final: 0.5533 (p90) REVERT: D 566 MET cc_start: 0.6793 (ttp) cc_final: 0.6194 (ptm) REVERT: D 625 ARG cc_start: 0.8171 (mmt180) cc_final: 0.7943 (mmm160) REVERT: D 724 MET cc_start: 0.8756 (mmm) cc_final: 0.8324 (mmm) REVERT: D 754 MET cc_start: 0.9129 (tmm) cc_final: 0.8843 (tmm) REVERT: D 783 MET cc_start: 0.9203 (mmt) cc_final: 0.8995 (mmm) REVERT: D 886 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9180 (mppt) REVERT: D 1054 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.5625 (mpp-170) REVERT: D 1143 MET cc_start: -0.1517 (ttp) cc_final: -0.2211 (ttp) REVERT: D 1153 MET cc_start: 0.7924 (ptt) cc_final: 0.7478 (pmm) outliers start: 101 outliers final: 80 residues processed: 314 average time/residue: 0.3938 time to fit residues: 199.1194 Evaluate side-chains 319 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 231 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 810 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 828 MET Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 998 HIS Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1131 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1043 LYS Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 850 CYS Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 997 ARG Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1056 LYS Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 509 VAL Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 833 ASP Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1086 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 9.9990 chunk 140 optimal weight: 0.9990 chunk 209 optimal weight: 0.0270 chunk 105 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 223 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 173 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 GLN B 94 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29110 Z= 0.159 Angle : 0.598 12.217 39479 Z= 0.291 Chirality : 0.042 0.217 4386 Planarity : 0.004 0.051 5173 Dihedral : 6.493 79.591 4219 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.13 % Favored : 93.79 % Rotamer: Outliers : 2.56 % Allowed : 18.45 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3653 helix: 1.56 (0.14), residues: 1464 sheet: 0.07 (0.23), residues: 559 loop : -1.36 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 607 HIS 0.006 0.001 HIS D 574 PHE 0.013 0.001 PHE D1078 TYR 0.013 0.001 TYR B 261 ARG 0.005 0.000 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 251 time to evaluate : 3.209 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: A 75 MET cc_start: 0.8658 (mtm) cc_final: 0.8289 (mtm) REVERT: A 149 MET cc_start: 0.8936 (mmp) cc_final: 0.8734 (mmt) REVERT: A 375 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: A 401 GLU cc_start: 0.8451 (pm20) cc_final: 0.8005 (pm20) REVERT: A 472 LEU cc_start: 0.9561 (tp) cc_final: 0.9357 (mm) REVERT: A 501 LEU cc_start: 0.9664 (mm) cc_final: 0.9452 (mm) REVERT: A 508 MET cc_start: 0.8832 (mmm) cc_final: 0.8370 (mmm) REVERT: A 577 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8602 (mm) REVERT: A 822 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8566 (pp) REVERT: B 41 MET cc_start: 0.7033 (ttp) cc_final: 0.5190 (tmm) REVERT: B 47 GLU cc_start: 0.7990 (pm20) cc_final: 0.6872 (pm20) REVERT: B 149 MET cc_start: 0.7895 (tmm) cc_final: 0.7682 (tmm) REVERT: B 377 ARG cc_start: 0.7059 (mtm-85) cc_final: 0.6791 (mtm180) REVERT: B 379 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8704 (t) REVERT: B 428 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8553 (mtmt) REVERT: B 671 MET cc_start: 0.6479 (tpt) cc_final: 0.5573 (tpt) REVERT: B 801 MET cc_start: 0.9008 (mtt) cc_final: 0.8628 (mtm) REVERT: B 921 MET cc_start: 0.8969 (mtp) cc_final: 0.8732 (mpp) REVERT: B 994 LEU cc_start: 0.9389 (mt) cc_final: 0.9080 (pp) REVERT: B 1006 ASP cc_start: 0.9344 (m-30) cc_final: 0.8906 (m-30) REVERT: B 1097 GLU cc_start: 0.2043 (OUTLIER) cc_final: 0.1173 (pm20) REVERT: B 1165 ASP cc_start: 0.9038 (t0) cc_final: 0.8582 (m-30) REVERT: C 566 MET cc_start: 0.8521 (ptm) cc_final: 0.8318 (ptm) REVERT: C 616 MET cc_start: 0.8600 (mmm) cc_final: 0.8203 (mmp) REVERT: C 619 LEU cc_start: 0.9062 (mm) cc_final: 0.8859 (mp) REVERT: C 801 MET cc_start: 0.8741 (tpp) cc_final: 0.8378 (mtt) REVERT: C 854 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6536 (tpt) REVERT: C 1036 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7932 (ptm-80) REVERT: C 1048 PHE cc_start: 0.5863 (OUTLIER) cc_final: 0.5493 (p90) REVERT: D 566 MET cc_start: 0.6885 (ttp) cc_final: 0.6142 (ptm) REVERT: D 724 MET cc_start: 0.8742 (mmm) cc_final: 0.8279 (mmm) REVERT: D 754 MET cc_start: 0.9102 (tmm) cc_final: 0.8788 (tmm) REVERT: D 783 MET cc_start: 0.9160 (mmt) cc_final: 0.8936 (mmm) REVERT: D 810 MET cc_start: 0.8822 (mmm) cc_final: 0.8601 (mmm) REVERT: D 854 MET cc_start: 0.8314 (tpt) cc_final: 0.7967 (tpt) REVERT: D 1054 ARG cc_start: 0.6263 (OUTLIER) cc_final: 0.5535 (mpp-170) REVERT: D 1143 MET cc_start: -0.1675 (ttp) cc_final: -0.2275 (ttp) REVERT: D 1153 MET cc_start: 0.7875 (ptt) cc_final: 0.7452 (pmm) outliers start: 77 outliers final: 55 residues processed: 312 average time/residue: 0.4069 time to fit residues: 201.8450 Evaluate side-chains 304 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 241 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1097 GLU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 854 MET Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 997 ARG Chi-restraints excluded: chain C residue 1008 LEU Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1054 ARG Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1086 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 326 optimal weight: 0.9980 chunk 196 optimal weight: 0.0170 chunk 142 optimal weight: 10.0000 chunk 256 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 295 optimal weight: 20.0000 chunk 309 optimal weight: 4.9990 chunk 325 optimal weight: 10.0000 overall best weight: 3.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 HIS A1075 GLN A1161 HIS ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN B 330 GLN B 421 HIS B 479 GLN B 879 HIS ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 873 ASN ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29110 Z= 0.339 Angle : 0.715 14.177 39479 Z= 0.359 Chirality : 0.044 0.207 4386 Planarity : 0.005 0.060 5173 Dihedral : 6.801 81.619 4215 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.88 % Favored : 91.98 % Rotamer: Outliers : 2.99 % Allowed : 18.42 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.14), residues: 3653 helix: 1.16 (0.14), residues: 1475 sheet: -0.13 (0.22), residues: 561 loop : -1.45 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 607 HIS 0.008 0.001 HIS A 998 PHE 0.023 0.002 PHE A 387 TYR 0.025 0.002 TYR A 118 ARG 0.014 0.001 ARG B1070 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 228 time to evaluate : 4.305 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: A 75 MET cc_start: 0.8726 (mtm) cc_final: 0.8378 (mtm) REVERT: A 149 MET cc_start: 0.8974 (mmp) cc_final: 0.8730 (mmt) REVERT: A 276 GLU cc_start: 0.7394 (mp0) cc_final: 0.6807 (mp0) REVERT: A 375 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: A 401 GLU cc_start: 0.8513 (pm20) cc_final: 0.8035 (pm20) REVERT: A 508 MET cc_start: 0.8854 (mmm) cc_final: 0.8509 (mmm) REVERT: A 577 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8895 (mm) REVERT: A 607 TRP cc_start: 0.7692 (OUTLIER) cc_final: 0.6606 (t60) REVERT: A 822 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8574 (pp) REVERT: B 41 MET cc_start: 0.7470 (ttp) cc_final: 0.7160 (tmm) REVERT: B 47 GLU cc_start: 0.8133 (pm20) cc_final: 0.7093 (pm20) REVERT: B 149 MET cc_start: 0.7930 (tmm) cc_final: 0.7679 (tmm) REVERT: B 377 ARG cc_start: 0.7092 (mtm-85) cc_final: 0.6862 (mtm180) REVERT: B 379 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8781 (t) REVERT: B 428 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8565 (mtmt) REVERT: B 686 MET cc_start: 0.8499 (mmt) cc_final: 0.8262 (mmt) REVERT: B 801 MET cc_start: 0.9073 (mtt) cc_final: 0.8792 (mtm) REVERT: B 836 GLU cc_start: 0.8910 (tp30) cc_final: 0.8672 (tp30) REVERT: B 994 LEU cc_start: 0.9419 (mt) cc_final: 0.9127 (pp) REVERT: B 1006 ASP cc_start: 0.9348 (m-30) cc_final: 0.8983 (m-30) REVERT: B 1143 MET cc_start: 0.2163 (tpt) cc_final: 0.1594 (tpt) REVERT: B 1145 MET cc_start: 0.5468 (ptp) cc_final: 0.4435 (ptt) REVERT: B 1165 ASP cc_start: 0.9104 (t0) cc_final: 0.8793 (m-30) REVERT: C 566 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8250 (ptm) REVERT: C 616 MET cc_start: 0.8703 (mmm) cc_final: 0.8357 (mmp) REVERT: C 801 MET cc_start: 0.8792 (tpp) cc_final: 0.8523 (mtt) REVERT: C 1038 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8135 (p90) REVERT: D 566 MET cc_start: 0.6854 (ttp) cc_final: 0.6239 (ptm) REVERT: D 724 MET cc_start: 0.8868 (mmm) cc_final: 0.8663 (mmm) REVERT: D 754 MET cc_start: 0.9135 (tmm) cc_final: 0.8910 (tmm) REVERT: D 881 MET cc_start: 0.9031 (mmt) cc_final: 0.8707 (mtt) REVERT: D 900 MET cc_start: 0.9079 (ppp) cc_final: 0.8621 (ppp) REVERT: D 1143 MET cc_start: -0.0985 (ttp) cc_final: -0.1706 (ttp) REVERT: D 1153 MET cc_start: 0.7918 (ptt) cc_final: 0.7404 (pmm) outliers start: 90 outliers final: 68 residues processed: 294 average time/residue: 0.4086 time to fit residues: 193.0707 Evaluate side-chains 300 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 225 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 656 ASP Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 987 LEU Chi-restraints excluded: chain C residue 997 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1137 LEU Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1145 MET Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1076 VAL Chi-restraints excluded: chain D residue 1084 LEU Chi-restraints excluded: chain D residue 1086 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.0570 chunk 345 optimal weight: 0.0980 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 362 optimal weight: 9.9990 chunk 333 optimal weight: 2.9990 chunk 288 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1075 GLN ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 GLN ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 873 ASN ** D 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29110 Z= 0.177 Angle : 0.641 13.035 39479 Z= 0.312 Chirality : 0.043 0.231 4386 Planarity : 0.004 0.044 5173 Dihedral : 6.582 85.879 4215 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.32 % Favored : 93.57 % Rotamer: Outliers : 2.09 % Allowed : 19.45 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3653 helix: 1.41 (0.14), residues: 1475 sheet: -0.08 (0.22), residues: 566 loop : -1.34 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 607 HIS 0.012 0.001 HIS D1059 PHE 0.013 0.001 PHE A 387 TYR 0.015 0.001 TYR B 261 ARG 0.008 0.000 ARG D 625 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7306 Ramachandran restraints generated. 3653 Oldfield, 0 Emsley, 3653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 248 time to evaluate : 2.900 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 75 MET cc_start: 0.8730 (mtm) cc_final: 0.8368 (mtm) REVERT: A 276 GLU cc_start: 0.7506 (mp0) cc_final: 0.6866 (mp0) REVERT: A 375 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: A 401 GLU cc_start: 0.8435 (pm20) cc_final: 0.8034 (pm20) REVERT: A 508 MET cc_start: 0.8852 (mmm) cc_final: 0.8463 (mmm) REVERT: A 577 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8618 (mm) REVERT: A 607 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.6681 (t60) REVERT: A 822 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8498 (pp) REVERT: B 41 MET cc_start: 0.7414 (ttp) cc_final: 0.5599 (tmm) REVERT: B 149 MET cc_start: 0.7975 (tmm) cc_final: 0.7727 (tmm) REVERT: B 234 PHE cc_start: 0.9179 (m-10) cc_final: 0.8967 (m-10) REVERT: B 250 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8816 (pp) REVERT: B 377 ARG cc_start: 0.7018 (mtm-85) cc_final: 0.6731 (mtm180) REVERT: B 379 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8741 (t) REVERT: B 671 MET cc_start: 0.6617 (tpt) cc_final: 0.5620 (tpt) REVERT: B 686 MET cc_start: 0.8371 (mmt) cc_final: 0.8109 (mmt) REVERT: B 801 MET cc_start: 0.8962 (mtt) cc_final: 0.8646 (mtm) REVERT: B 921 MET cc_start: 0.8947 (mtp) cc_final: 0.8686 (mpp) REVERT: B 994 LEU cc_start: 0.9439 (mt) cc_final: 0.9126 (pp) REVERT: B 1006 ASP cc_start: 0.9349 (m-30) cc_final: 0.8948 (m-30) REVERT: B 1143 MET cc_start: 0.2087 (tpt) cc_final: 0.1730 (tpt) REVERT: B 1165 ASP cc_start: 0.9111 (t0) cc_final: 0.8798 (m-30) REVERT: C 616 MET cc_start: 0.8589 (mmm) cc_final: 0.8191 (mmp) REVERT: C 801 MET cc_start: 0.8677 (tpp) cc_final: 0.8462 (mtt) REVERT: D 724 MET cc_start: 0.8795 (mmm) cc_final: 0.8357 (mmm) REVERT: D 754 MET cc_start: 0.9075 (tmm) cc_final: 0.8825 (tmm) REVERT: D 810 MET cc_start: 0.8841 (mmm) cc_final: 0.8638 (mmm) REVERT: D 854 MET cc_start: 0.8404 (tpt) cc_final: 0.8145 (tpt) REVERT: D 881 MET cc_start: 0.8947 (mmt) cc_final: 0.8580 (mtt) REVERT: D 1143 MET cc_start: -0.1438 (ttp) cc_final: -0.2154 (ttp) REVERT: D 1153 MET cc_start: 0.7955 (ptt) cc_final: 0.7523 (pmm) outliers start: 63 outliers final: 53 residues processed: 298 average time/residue: 0.4138 time to fit residues: 199.2307 Evaluate side-chains 293 residues out of total 3013 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 234 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 607 TRP Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 1057 THR Chi-restraints excluded: chain A residue 1166 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 629 GLU Chi-restraints excluded: chain B residue 647 ASN Chi-restraints excluded: chain B residue 651 TYR Chi-restraints excluded: chain B residue 677 PHE Chi-restraints excluded: chain B residue 908 THR Chi-restraints excluded: chain B residue 910 SER Chi-restraints excluded: chain B residue 1033 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 607 TRP Chi-restraints excluded: chain C residue 677 PHE Chi-restraints excluded: chain C residue 686 MET Chi-restraints excluded: chain C residue 704 ILE Chi-restraints excluded: chain C residue 752 CYS Chi-restraints excluded: chain C residue 828 MET Chi-restraints excluded: chain C residue 848 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 952 ILE Chi-restraints excluded: chain C residue 997 ARG Chi-restraints excluded: chain C residue 1038 PHE Chi-restraints excluded: chain C residue 1054 ARG Chi-restraints excluded: chain C residue 1144 LYS Chi-restraints excluded: chain C residue 1147 THR Chi-restraints excluded: chain C residue 1177 ILE Chi-restraints excluded: chain D residue 513 THR Chi-restraints excluded: chain D residue 525 THR Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 647 ASN Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 752 CYS Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 813 LEU Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 826 VAL Chi-restraints excluded: chain D residue 954 VAL Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1086 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 0.9990 chunk 307 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 289 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 296 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 864 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.070893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.053739 restraints weight = 162147.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.055361 restraints weight = 102308.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.056487 restraints weight = 74032.975| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29110 Z= 0.203 Angle : 0.647 12.390 39479 Z= 0.314 Chirality : 0.042 0.226 4386 Planarity : 0.004 0.130 5173 Dihedral : 6.524 87.356 4215 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.36 % Favored : 92.55 % Rotamer: Outliers : 2.09 % Allowed : 19.85 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.02 (0.14), residues: 3653 helix: 1.44 (0.14), residues: 1472 sheet: -0.09 (0.22), residues: 570 loop : -1.31 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 607 HIS 0.005 0.001 HIS A 998 PHE 0.013 0.001 PHE A 387 TYR 0.015 0.001 TYR A 118 ARG 0.028 0.000 ARG A 942 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5605.67 seconds wall clock time: 103 minutes 36.38 seconds (6216.38 seconds total)