Starting phenix.real_space_refine on Sat Jul 20 18:28:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3v_36862/07_2024/8k3v_36862_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3v_36862/07_2024/8k3v_36862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3v_36862/07_2024/8k3v_36862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3v_36862/07_2024/8k3v_36862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3v_36862/07_2024/8k3v_36862_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3v_36862/07_2024/8k3v_36862_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 7366 2.51 5 N 1802 2.21 5 O 2000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 610": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1060": "OE1" <-> "OE2" Residue "A GLU 1086": "OE1" <-> "OE2" Residue "A TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B ASP 488": "OD1" <-> "OD2" Residue "B TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 610": "OD1" <-> "OD2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B ASP 661": "OD1" <-> "OD2" Residue "B GLU 665": "OE1" <-> "OE2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "B ASP 717": "OD1" <-> "OD2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 862": "OE1" <-> "OE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1015": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1060": "OE1" <-> "OE2" Residue "B GLU 1086": "OE1" <-> "OE2" Residue "B TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11248 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5536 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 20, 'TRANS': 679} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 5536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5536 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 20, 'TRANS': 679} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 108 Chain: "A" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 136 Unusual residues: {' MG': 1, 'POV': 2, 'UD1': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' MG': 1, 'UD1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.13, per 1000 atoms: 0.63 Number of scatterers: 11248 At special positions: 0 Unit cell: (132.5, 92.22, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 6 15.00 Mg 2 11.99 O 2000 8.00 N 1802 7.00 C 7366 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.53 Conformation dependent library (CDL) restraints added in 2.0 seconds 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2668 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 64.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.610A pdb=" N PHE A 413 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.862A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 478 removed outlier: 3.516A pdb=" N LEU A 462 " --> pdb=" O ASP A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 removed outlier: 3.550A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 5.908A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 669 removed outlier: 3.633A pdb=" N SER A 649 " --> pdb=" O PRO A 645 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 removed outlier: 3.831A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.749A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 removed outlier: 4.074A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 781 removed outlier: 3.564A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.736A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.553A pdb=" N LEU A 834 " --> pdb=" O ALA A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 894 removed outlier: 3.956A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 932 removed outlier: 4.529A pdb=" N ILE A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 915 " --> pdb=" O PHE A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.549A pdb=" N SER A 941 " --> pdb=" O HIS A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 949 through 955 Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.586A pdb=" N ILE A1001 " --> pdb=" O SER A 997 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A1005 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A1007 " --> pdb=" O ALA A1003 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1060 Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1091 through 1127 removed outlier: 4.200A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 410 through 413 removed outlier: 3.610A pdb=" N PHE B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 413' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.862A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 458 through 478 removed outlier: 3.516A pdb=" N LEU B 462 " --> pdb=" O ASP B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 517 removed outlier: 3.551A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.554A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 4.033A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 5.909A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 669 removed outlier: 3.632A pdb=" N SER B 649 " --> pdb=" O PRO B 645 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 removed outlier: 3.831A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.749A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 removed outlier: 4.074A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.565A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.529A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.736A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 removed outlier: 3.553A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 894 removed outlier: 3.956A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 932 removed outlier: 4.529A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 915 " --> pdb=" O PHE B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.549A pdb=" N SER B 941 " --> pdb=" O HIS B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 948 Processing helix chain 'B' and resid 949 through 955 Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 997 through 1012 removed outlier: 3.586A pdb=" N ILE B1001 " --> pdb=" O SER B 997 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR B1005 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS B1007 " --> pdb=" O ALA B1003 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR B1008 " --> pdb=" O ASN B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1060 Processing helix chain 'B' and resid 1063 through 1074 Processing helix chain 'B' and resid 1091 through 1127 removed outlier: 4.200A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.694A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET A 449 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU A 601 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 451 " --> pdb=" O LEU A 601 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS A 735 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA A 627 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS A 737 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY A 629 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N SER A 739 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ILE A 631 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TYR A 741 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N THR A 633 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER A 743 " --> pdb=" O THR A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.670A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.693A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET B 449 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU B 601 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL B 451 " --> pdb=" O LEU B 601 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LYS B 735 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 627 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS B 737 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY B 629 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N SER B 739 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 9.878A pdb=" N ILE B 631 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N TYR B 741 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 9.951A pdb=" N THR B 633 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER B 743 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.671A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 4.97 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: 1706 1.31 - 1.43: 3298 1.43 - 1.56: 6390 1.56 - 1.69: 12 1.69 - 1.81: 112 Bond restraints: 11518 Sorted by residual: bond pdb=" C4 UD1 A1503 " pdb=" N3 UD1 A1503 " ideal model delta sigma weight residual 1.386 1.277 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C4 UD1 B1502 " pdb=" N3 UD1 B1502 " ideal model delta sigma weight residual 1.386 1.278 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C2B UD1 A1503 " pdb=" C3B UD1 A1503 " ideal model delta sigma weight residual 1.533 1.461 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2B UD1 B1502 " pdb=" C3B UD1 B1502 " ideal model delta sigma weight residual 1.533 1.462 0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C4 UD1 B1502 " pdb=" C5 UD1 B1502 " ideal model delta sigma weight residual 1.441 1.377 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 11513 not shown) Histogram of bond angle deviations from ideal: 91.14 - 99.77: 4 99.77 - 108.41: 515 108.41 - 117.04: 7329 117.04 - 125.68: 7582 125.68 - 134.31: 180 Bond angle restraints: 15610 Sorted by residual: angle pdb=" C1B UD1 A1503 " pdb=" C2B UD1 A1503 " pdb=" O2' UD1 A1503 " ideal model delta sigma weight residual 109.46 130.39 -20.93 3.00e+00 1.11e-01 4.87e+01 angle pdb=" C1B UD1 B1502 " pdb=" C2B UD1 B1502 " pdb=" O2' UD1 B1502 " ideal model delta sigma weight residual 109.46 130.38 -20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" C2B UD1 B1502 " pdb=" C1B UD1 B1502 " pdb=" O4B UD1 B1502 " ideal model delta sigma weight residual 106.74 91.14 15.60 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C2B UD1 A1503 " pdb=" C1B UD1 A1503 " pdb=" O4B UD1 A1503 " ideal model delta sigma weight residual 106.74 91.15 15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" N ARG B 912 " pdb=" CA ARG B 912 " pdb=" C ARG B 912 " ideal model delta sigma weight residual 112.54 106.72 5.82 1.22e+00 6.72e-01 2.28e+01 ... (remaining 15605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.01: 6543 33.01 - 66.02: 243 66.02 - 99.04: 32 99.04 - 132.05: 6 132.05 - 165.06: 2 Dihedral angle restraints: 6826 sinusoidal: 2702 harmonic: 4124 Sorted by residual: dihedral pdb=" C27 POV A1502 " pdb=" C28 POV A1502 " pdb=" C29 POV A1502 " pdb="C210 POV A1502 " ideal model delta sinusoidal sigma weight residual 127.48 -67.46 -165.06 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C27 POV A1504 " pdb=" C28 POV A1504 " pdb=" C29 POV A1504 " pdb="C210 POV A1504 " ideal model delta sinusoidal sigma weight residual 127.48 -67.55 -164.97 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA ALA A 715 " pdb=" C ALA A 715 " pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta harmonic sigma weight residual 180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 6823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1526 0.090 - 0.181: 214 0.181 - 0.271: 20 0.271 - 0.362: 6 0.362 - 0.452: 4 Chirality restraints: 1770 Sorted by residual: chirality pdb=" C2B UD1 B1502 " pdb=" C1B UD1 B1502 " pdb=" C3B UD1 B1502 " pdb=" O2' UD1 B1502 " both_signs ideal model delta sigma weight residual False -2.62 -2.17 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C2B UD1 A1503 " pdb=" C1B UD1 A1503 " pdb=" C3B UD1 A1503 " pdb=" O2' UD1 A1503 " both_signs ideal model delta sigma weight residual False -2.62 -2.17 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C5' UD1 B1502 " pdb=" C4' UD1 B1502 " pdb=" C6' UD1 B1502 " pdb=" O5' UD1 B1502 " both_signs ideal model delta sigma weight residual False -2.52 -2.10 -0.42 2.00e-01 2.50e+01 4.40e+00 ... (remaining 1767 not shown) Planarity restraints: 1900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2' UD1 A1503 " 0.170 2.00e-02 2.50e+03 1.37e-01 2.33e+02 pdb=" C7' UD1 A1503 " -0.055 2.00e-02 2.50e+03 pdb=" C8' UD1 A1503 " 0.133 2.00e-02 2.50e+03 pdb=" N2' UD1 A1503 " -0.205 2.00e-02 2.50e+03 pdb=" O7' UD1 A1503 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2' UD1 B1502 " 0.169 2.00e-02 2.50e+03 1.37e-01 2.33e+02 pdb=" C7' UD1 B1502 " -0.054 2.00e-02 2.50e+03 pdb=" C8' UD1 B1502 " 0.133 2.00e-02 2.50e+03 pdb=" N2' UD1 B1502 " -0.205 2.00e-02 2.50e+03 pdb=" O7' UD1 B1502 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A1502 " -0.041 2.00e-02 2.50e+03 7.55e-02 5.70e+01 pdb=" C29 POV A1502 " 0.099 2.00e-02 2.50e+03 pdb="C210 POV A1502 " -0.099 2.00e-02 2.50e+03 pdb="C211 POV A1502 " 0.040 2.00e-02 2.50e+03 ... (remaining 1897 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1947 2.76 - 3.30: 11091 3.30 - 3.83: 18126 3.83 - 4.37: 21569 4.37 - 4.90: 38362 Nonbonded interactions: 91095 Sorted by model distance: nonbonded pdb=" O HIS B 706 " pdb=" OG SER B 710 " model vdw 2.227 2.440 nonbonded pdb=" O HIS A 706 " pdb=" OG SER A 710 " model vdw 2.227 2.440 nonbonded pdb=" O3' UD1 B1502 " pdb=" O7' UD1 B1502 " model vdw 2.284 2.440 nonbonded pdb=" O3' UD1 A1503 " pdb=" O7' UD1 A1503 " model vdw 2.284 2.440 nonbonded pdb=" O THR B 453 " pdb=" O3B UD1 B1502 " model vdw 2.307 2.440 ... (remaining 91090 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 381 through 1127 or resid 1501)) selection = (chain 'B' and (resid 381 through 1127 or resid 1501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 33.900 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 0.109 11518 Z= 0.517 Angle : 1.065 20.927 15610 Z= 0.623 Chirality : 0.066 0.452 1770 Planarity : 0.006 0.137 1900 Dihedral : 17.586 165.061 4158 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.91 % Allowed : 2.37 % Favored : 92.72 % Cbeta Deviations : 0.15 % 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: -0.31 (0.22), residues: 1376 helix: 0.99 (0.19), residues: 760 sheet: -1.44 (0.47), residues: 112 loop : -1.77 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 779 HIS 0.004 0.001 HIS B 783 PHE 0.020 0.002 PHE B 885 TYR 0.040 0.002 TYR B 696 ARG 0.005 0.001 ARG B 718 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 172 time to evaluate : 1.281 Fit side-chains REVERT: A 455 TYR cc_start: 0.8101 (t80) cc_final: 0.7559 (t80) REVERT: A 471 ASP cc_start: 0.7287 (m-30) cc_final: 0.6795 (m-30) REVERT: A 610 ASP cc_start: 0.7777 (t70) cc_final: 0.7238 (t0) REVERT: A 672 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8145 (t) REVERT: A 989 THR cc_start: 0.5520 (OUTLIER) cc_final: 0.5282 (p) REVERT: A 991 LYS cc_start: 0.3042 (OUTLIER) cc_final: 0.2651 (mmtt) REVERT: A 992 MET cc_start: 0.0382 (OUTLIER) cc_final: 0.0090 (pmm) REVERT: A 998 SER cc_start: 0.4331 (OUTLIER) cc_final: 0.3757 (t) REVERT: B 416 MET cc_start: 0.7878 (tmm) cc_final: 0.7641 (tmm) REVERT: B 455 TYR cc_start: 0.8127 (t80) cc_final: 0.7661 (t80) REVERT: B 464 ARG cc_start: 0.7684 (mtm-85) cc_final: 0.7174 (mtp-110) REVERT: B 471 ASP cc_start: 0.7176 (m-30) cc_final: 0.6794 (m-30) REVERT: B 610 ASP cc_start: 0.7753 (t70) cc_final: 0.7237 (t0) REVERT: B 700 MET cc_start: 0.5425 (tmm) cc_final: 0.5097 (tmm) REVERT: B 998 SER cc_start: 0.3779 (OUTLIER) cc_final: 0.3309 (t) outliers start: 58 outliers final: 13 residues processed: 206 average time/residue: 0.2675 time to fit residues: 76.8022 Evaluate side-chains 140 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 880 ILE Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 986 GLU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 992 MET Chi-restraints excluded: chain A residue 998 SER Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 780 SER Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain B residue 998 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 HIS A 692 GLN A1004 ASN B 540 HIS B 706 HIS B1004 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11518 Z= 0.203 Angle : 0.512 6.219 15610 Z= 0.276 Chirality : 0.040 0.140 1770 Planarity : 0.004 0.045 1900 Dihedral : 10.805 100.951 1732 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.28 % Allowed : 7.11 % Favored : 90.61 % 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: 0.88 (0.23), residues: 1376 helix: 1.82 (0.19), residues: 786 sheet: -0.57 (0.43), residues: 142 loop : -1.26 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 779 HIS 0.003 0.001 HIS B 828 PHE 0.018 0.002 PHE B1052 TYR 0.011 0.001 TYR A 925 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.253 Fit side-chains REVERT: A 455 TYR cc_start: 0.7951 (t80) cc_final: 0.7376 (t80) REVERT: A 471 ASP cc_start: 0.7091 (m-30) cc_final: 0.6779 (m-30) REVERT: A 641 LYS cc_start: 0.8233 (mttm) cc_final: 0.7631 (mtmt) REVERT: A 859 LYS cc_start: 0.8583 (mmmm) cc_final: 0.8357 (mppt) REVERT: A 989 THR cc_start: 0.5729 (OUTLIER) cc_final: 0.5475 (p) REVERT: A 991 LYS cc_start: 0.3258 (OUTLIER) cc_final: 0.2473 (mttm) REVERT: B 455 TYR cc_start: 0.8022 (t80) cc_final: 0.7490 (t80) REVERT: B 471 ASP cc_start: 0.7134 (m-30) cc_final: 0.6817 (m-30) REVERT: B 641 LYS cc_start: 0.8227 (mttm) cc_final: 0.7622 (mtmt) REVERT: B 700 MET cc_start: 0.5634 (tmm) cc_final: 0.5396 (tmm) REVERT: B 859 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8325 (mppt) REVERT: B 982 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6949 (mp) outliers start: 27 outliers final: 12 residues processed: 142 average time/residue: 0.2722 time to fit residues: 54.4938 Evaluate side-chains 125 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 985 THR Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 127 optimal weight: 0.3980 chunk 137 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN B1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11518 Z= 0.179 Angle : 0.460 7.767 15610 Z= 0.248 Chirality : 0.039 0.137 1770 Planarity : 0.003 0.044 1900 Dihedral : 9.161 77.587 1709 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.69 % Allowed : 10.58 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.23), residues: 1376 helix: 2.31 (0.19), residues: 786 sheet: -0.37 (0.43), residues: 148 loop : -1.11 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 779 HIS 0.002 0.001 HIS B 828 PHE 0.017 0.001 PHE B1052 TYR 0.009 0.001 TYR A 925 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.332 Fit side-chains REVERT: A 455 TYR cc_start: 0.8092 (t80) cc_final: 0.7670 (t80) REVERT: A 471 ASP cc_start: 0.7062 (m-30) cc_final: 0.6786 (m-30) REVERT: A 641 LYS cc_start: 0.8242 (mttm) cc_final: 0.7647 (mtmt) REVERT: A 982 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6762 (mp) REVERT: A 989 THR cc_start: 0.5715 (OUTLIER) cc_final: 0.5444 (p) REVERT: A 991 LYS cc_start: 0.3154 (OUTLIER) cc_final: 0.2544 (mttm) REVERT: A 1105 VAL cc_start: 0.8218 (t) cc_final: 0.8008 (p) REVERT: B 455 TYR cc_start: 0.8112 (t80) cc_final: 0.7690 (t80) REVERT: B 464 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7199 (mtp180) REVERT: B 471 ASP cc_start: 0.7076 (m-30) cc_final: 0.6819 (m-30) REVERT: B 641 LYS cc_start: 0.8301 (mttm) cc_final: 0.7685 (mtmt) REVERT: B 700 MET cc_start: 0.5710 (tmm) cc_final: 0.5382 (tmm) REVERT: B 859 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8385 (mppt) REVERT: B 938 MET cc_start: 0.6540 (tpt) cc_final: 0.5930 (tpt) REVERT: B 982 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6921 (mp) REVERT: B 1105 VAL cc_start: 0.8216 (t) cc_final: 0.7993 (p) outliers start: 20 outliers final: 9 residues processed: 146 average time/residue: 0.2659 time to fit residues: 54.3135 Evaluate side-chains 129 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 559 ASN Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 66 optimal weight: 0.0470 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 0.0000 chunk 85 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 135 optimal weight: 0.0970 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 ASN B1004 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11518 Z= 0.125 Angle : 0.416 8.408 15610 Z= 0.223 Chirality : 0.038 0.127 1770 Planarity : 0.003 0.041 1900 Dihedral : 8.579 75.097 1702 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.35 % Allowed : 11.59 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.23), residues: 1376 helix: 2.76 (0.19), residues: 784 sheet: 0.07 (0.45), residues: 148 loop : -1.04 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 779 HIS 0.001 0.000 HIS B 828 PHE 0.012 0.001 PHE A1052 TYR 0.009 0.001 TYR B 827 ARG 0.002 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.350 Fit side-chains REVERT: A 455 TYR cc_start: 0.8104 (t80) cc_final: 0.7801 (t80) REVERT: A 471 ASP cc_start: 0.7098 (m-30) cc_final: 0.6805 (m-30) REVERT: A 641 LYS cc_start: 0.8262 (mttm) cc_final: 0.7657 (mtmt) REVERT: A 771 SER cc_start: 0.8597 (p) cc_final: 0.8379 (m) REVERT: A 989 THR cc_start: 0.5924 (OUTLIER) cc_final: 0.5642 (p) REVERT: A 991 LYS cc_start: 0.2846 (OUTLIER) cc_final: 0.2303 (mttm) REVERT: A 1120 MET cc_start: 0.8013 (tpp) cc_final: 0.7714 (mmt) REVERT: B 417 ARG cc_start: 0.7013 (ttt180) cc_final: 0.6684 (ttm170) REVERT: B 455 TYR cc_start: 0.8147 (t80) cc_final: 0.7786 (t80) REVERT: B 464 ARG cc_start: 0.7519 (mtm-85) cc_final: 0.7086 (mtp180) REVERT: B 471 ASP cc_start: 0.7108 (m-30) cc_final: 0.6832 (m-30) REVERT: B 529 ASN cc_start: 0.7374 (m-40) cc_final: 0.7135 (m-40) REVERT: B 641 LYS cc_start: 0.8260 (mttm) cc_final: 0.7658 (mtmt) REVERT: B 700 MET cc_start: 0.5674 (tmm) cc_final: 0.5373 (tmm) REVERT: B 771 SER cc_start: 0.8617 (p) cc_final: 0.8399 (m) REVERT: B 859 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8384 (mppt) REVERT: B 982 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6868 (mp) REVERT: B 1120 MET cc_start: 0.7997 (tpp) cc_final: 0.7712 (mmt) outliers start: 16 outliers final: 4 residues processed: 143 average time/residue: 0.2745 time to fit residues: 54.4461 Evaluate side-chains 124 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 982 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 0.0270 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A1004 ASN B 559 ASN B1004 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11518 Z= 0.266 Angle : 0.506 9.193 15610 Z= 0.269 Chirality : 0.041 0.145 1770 Planarity : 0.003 0.040 1900 Dihedral : 9.000 82.066 1700 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.37 % Allowed : 10.83 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.23), residues: 1376 helix: 2.44 (0.18), residues: 784 sheet: -0.18 (0.46), residues: 128 loop : -1.23 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS A 828 PHE 0.019 0.002 PHE B1052 TYR 0.019 0.001 TYR B 827 ARG 0.003 0.001 ARG A 749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.335 Fit side-chains REVERT: A 455 TYR cc_start: 0.8185 (t80) cc_final: 0.7909 (t80) REVERT: A 471 ASP cc_start: 0.7098 (m-30) cc_final: 0.6682 (m-30) REVERT: A 641 LYS cc_start: 0.8297 (mttm) cc_final: 0.7712 (mtmt) REVERT: A 758 ARG cc_start: 0.8611 (tmm160) cc_final: 0.8250 (ttt-90) REVERT: A 800 PHE cc_start: 0.7642 (t80) cc_final: 0.7441 (t80) REVERT: A 982 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6877 (mp) REVERT: A 989 THR cc_start: 0.5741 (OUTLIER) cc_final: 0.5460 (p) REVERT: A 991 LYS cc_start: 0.3152 (OUTLIER) cc_final: 0.2571 (ptpt) REVERT: A 1105 VAL cc_start: 0.8222 (t) cc_final: 0.8008 (p) REVERT: B 455 TYR cc_start: 0.8209 (t80) cc_final: 0.7909 (t80) REVERT: B 471 ASP cc_start: 0.7078 (m-30) cc_final: 0.6676 (m-30) REVERT: B 641 LYS cc_start: 0.8291 (mttm) cc_final: 0.7710 (mtmt) REVERT: B 700 MET cc_start: 0.5661 (tmm) cc_final: 0.5234 (tmm) REVERT: B 800 PHE cc_start: 0.7653 (t80) cc_final: 0.7452 (t80) REVERT: B 859 LYS cc_start: 0.8696 (mmmm) cc_final: 0.8422 (mppt) REVERT: B 982 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6802 (mp) REVERT: B 1009 LEU cc_start: 0.6175 (mp) cc_final: 0.5964 (mp) REVERT: B 1105 VAL cc_start: 0.8220 (t) cc_final: 0.8003 (p) outliers start: 28 outliers final: 10 residues processed: 144 average time/residue: 0.2714 time to fit residues: 54.3631 Evaluate side-chains 130 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 135 optimal weight: 0.0870 chunk 112 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN B 559 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11518 Z= 0.156 Angle : 0.443 9.818 15610 Z= 0.236 Chirality : 0.038 0.129 1770 Planarity : 0.003 0.038 1900 Dihedral : 8.655 73.196 1700 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.61 % Allowed : 12.61 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.23), residues: 1376 helix: 2.67 (0.18), residues: 784 sheet: -0.06 (0.46), residues: 128 loop : -1.18 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 779 HIS 0.002 0.001 HIS A 828 PHE 0.015 0.001 PHE B1052 TYR 0.021 0.001 TYR B 827 ARG 0.004 0.000 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.230 Fit side-chains REVERT: A 386 VAL cc_start: 0.7895 (m) cc_final: 0.7680 (t) REVERT: A 416 MET cc_start: 0.7883 (tmm) cc_final: 0.7395 (tmm) REVERT: A 455 TYR cc_start: 0.8171 (t80) cc_final: 0.7951 (t80) REVERT: A 471 ASP cc_start: 0.7073 (m-30) cc_final: 0.6635 (m-30) REVERT: A 641 LYS cc_start: 0.8269 (mttm) cc_final: 0.7701 (mtmt) REVERT: A 758 ARG cc_start: 0.8594 (tmm160) cc_final: 0.8239 (ttt-90) REVERT: A 989 THR cc_start: 0.5910 (OUTLIER) cc_final: 0.5670 (p) REVERT: A 991 LYS cc_start: 0.2841 (OUTLIER) cc_final: 0.2530 (ptpt) REVERT: A 1105 VAL cc_start: 0.8188 (t) cc_final: 0.7971 (p) REVERT: B 455 TYR cc_start: 0.8195 (t80) cc_final: 0.7887 (t80) REVERT: B 471 ASP cc_start: 0.7056 (m-30) cc_final: 0.6772 (m-30) REVERT: B 641 LYS cc_start: 0.8261 (mttm) cc_final: 0.7694 (mtmt) REVERT: B 700 MET cc_start: 0.5599 (tmm) cc_final: 0.5362 (tmm) REVERT: B 859 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8418 (mppt) REVERT: B 982 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6912 (mp) REVERT: B 1105 VAL cc_start: 0.8199 (t) cc_final: 0.7983 (p) outliers start: 19 outliers final: 11 residues processed: 134 average time/residue: 0.2593 time to fit residues: 48.9641 Evaluate side-chains 125 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 82 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 ASN A1004 ASN B 559 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11518 Z= 0.181 Angle : 0.459 11.469 15610 Z= 0.243 Chirality : 0.039 0.134 1770 Planarity : 0.003 0.037 1900 Dihedral : 8.618 74.493 1700 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.61 % Allowed : 12.94 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1376 helix: 2.68 (0.18), residues: 784 sheet: 0.04 (0.45), residues: 132 loop : -1.17 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.002 0.001 HIS A 828 PHE 0.017 0.001 PHE B1052 TYR 0.019 0.001 TYR B 827 ARG 0.004 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.288 Fit side-chains REVERT: A 386 VAL cc_start: 0.8009 (m) cc_final: 0.7773 (t) REVERT: A 471 ASP cc_start: 0.7074 (m-30) cc_final: 0.6633 (m-30) REVERT: A 641 LYS cc_start: 0.8277 (mttm) cc_final: 0.7715 (mtmt) REVERT: A 758 ARG cc_start: 0.8557 (tmm160) cc_final: 0.8215 (ttt-90) REVERT: A 989 THR cc_start: 0.5905 (OUTLIER) cc_final: 0.5674 (p) REVERT: A 991 LYS cc_start: 0.2843 (OUTLIER) cc_final: 0.2495 (ptpt) REVERT: A 1105 VAL cc_start: 0.8201 (t) cc_final: 0.7995 (p) REVERT: B 455 TYR cc_start: 0.8196 (t80) cc_final: 0.7979 (t80) REVERT: B 471 ASP cc_start: 0.7082 (m-30) cc_final: 0.6636 (m-30) REVERT: B 641 LYS cc_start: 0.8270 (mttm) cc_final: 0.7709 (mtmt) REVERT: B 700 MET cc_start: 0.5799 (tmm) cc_final: 0.5487 (tmm) REVERT: B 859 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8427 (mppt) REVERT: B 982 ILE cc_start: 0.7188 (OUTLIER) cc_final: 0.6904 (mp) REVERT: B 1105 VAL cc_start: 0.8197 (t) cc_final: 0.7992 (p) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.2502 time to fit residues: 45.0232 Evaluate side-chains 124 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.4980 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 129 optimal weight: 8.9990 overall best weight: 1.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11518 Z= 0.348 Angle : 0.569 12.730 15610 Z= 0.298 Chirality : 0.043 0.148 1770 Planarity : 0.004 0.036 1900 Dihedral : 9.284 78.013 1700 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.69 % Allowed : 13.28 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.23), residues: 1376 helix: 2.26 (0.18), residues: 784 sheet: -0.07 (0.42), residues: 152 loop : -1.42 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.007 0.002 HIS A 828 PHE 0.020 0.002 PHE A1052 TYR 0.022 0.002 TYR A 827 ARG 0.004 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.299 Fit side-chains REVERT: A 471 ASP cc_start: 0.7112 (m-30) cc_final: 0.6645 (m-30) REVERT: A 641 LYS cc_start: 0.8300 (mttm) cc_final: 0.7777 (mtmt) REVERT: A 989 THR cc_start: 0.5926 (OUTLIER) cc_final: 0.5621 (p) REVERT: A 991 LYS cc_start: 0.2919 (OUTLIER) cc_final: 0.2325 (ptpt) REVERT: B 471 ASP cc_start: 0.7113 (m-30) cc_final: 0.6645 (m-30) REVERT: B 641 LYS cc_start: 0.8295 (mttm) cc_final: 0.7751 (mtmt) REVERT: B 700 MET cc_start: 0.5842 (tmm) cc_final: 0.5524 (tmm) REVERT: B 859 LYS cc_start: 0.8742 (mmmm) cc_final: 0.8482 (mppt) REVERT: B 982 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6852 (mp) outliers start: 20 outliers final: 13 residues processed: 136 average time/residue: 0.2589 time to fit residues: 49.5452 Evaluate side-chains 126 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 712 MET Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 129 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11518 Z= 0.198 Angle : 0.481 11.174 15610 Z= 0.253 Chirality : 0.039 0.132 1770 Planarity : 0.003 0.041 1900 Dihedral : 8.815 73.692 1700 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.61 % Allowed : 13.45 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1376 helix: 2.52 (0.18), residues: 784 sheet: -0.11 (0.44), residues: 132 loop : -1.31 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.003 0.001 HIS A 828 PHE 0.017 0.001 PHE B1052 TYR 0.021 0.001 TYR B 827 ARG 0.009 0.001 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.295 Fit side-chains REVERT: A 471 ASP cc_start: 0.7100 (m-30) cc_final: 0.6642 (m-30) REVERT: A 641 LYS cc_start: 0.8282 (mttm) cc_final: 0.7728 (mtmt) REVERT: A 989 THR cc_start: 0.5878 (OUTLIER) cc_final: 0.5605 (p) REVERT: A 991 LYS cc_start: 0.2957 (OUTLIER) cc_final: 0.2403 (ptpt) REVERT: B 471 ASP cc_start: 0.7109 (m-30) cc_final: 0.6649 (m-30) REVERT: B 641 LYS cc_start: 0.8273 (mttm) cc_final: 0.7727 (mtmt) REVERT: B 700 MET cc_start: 0.5869 (tmm) cc_final: 0.5596 (tmm) REVERT: B 859 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8440 (mppt) REVERT: B 982 ILE cc_start: 0.7217 (OUTLIER) cc_final: 0.6957 (mp) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 0.2753 time to fit residues: 50.9382 Evaluate side-chains 125 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11518 Z= 0.208 Angle : 0.512 12.706 15610 Z= 0.262 Chirality : 0.040 0.133 1770 Planarity : 0.003 0.038 1900 Dihedral : 8.776 73.454 1700 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.52 % Allowed : 13.96 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1376 helix: 2.56 (0.18), residues: 784 sheet: -0.08 (0.44), residues: 132 loop : -1.31 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1047 HIS 0.004 0.001 HIS B 937 PHE 0.018 0.002 PHE B1052 TYR 0.018 0.001 TYR A 827 ARG 0.008 0.001 ARG A 759 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2752 Ramachandran restraints generated. 1376 Oldfield, 0 Emsley, 1376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.256 Fit side-chains REVERT: A 471 ASP cc_start: 0.7097 (m-30) cc_final: 0.6639 (m-30) REVERT: A 527 GLU cc_start: 0.7443 (pt0) cc_final: 0.7222 (pt0) REVERT: A 641 LYS cc_start: 0.8281 (mttm) cc_final: 0.7728 (mtmt) REVERT: A 989 THR cc_start: 0.5772 (OUTLIER) cc_final: 0.5521 (p) REVERT: A 991 LYS cc_start: 0.3181 (OUTLIER) cc_final: 0.2504 (ptpt) REVERT: B 471 ASP cc_start: 0.7104 (m-30) cc_final: 0.6645 (m-30) REVERT: B 641 LYS cc_start: 0.8292 (mttm) cc_final: 0.7729 (mtmt) REVERT: B 700 MET cc_start: 0.5726 (tmm) cc_final: 0.5496 (tmm) REVERT: B 982 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6968 (mp) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.2614 time to fit residues: 46.1361 Evaluate side-chains 124 residues out of total 1268 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 991 LYS Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain B residue 562 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 ASP Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1042 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125624 restraints weight = 12913.546| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.04 r_work: 0.3297 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11518 Z= 0.154 Angle : 0.453 10.335 15610 Z= 0.238 Chirality : 0.039 0.127 1770 Planarity : 0.003 0.037 1900 Dihedral : 8.582 71.410 1700 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.35 % Allowed : 13.96 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.23), residues: 1376 helix: 2.77 (0.18), residues: 784 sheet: -0.02 (0.44), residues: 132 loop : -1.21 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 806 HIS 0.003 0.001 HIS B 828 PHE 0.015 0.001 PHE B1052 TYR 0.019 0.001 TYR B 827 ARG 0.008 0.000 ARG A 759 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2462.32 seconds wall clock time: 46 minutes 20.21 seconds (2780.21 seconds total)