Starting phenix.real_space_refine on Tue Jul 23 15:12:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/07_2024/8pba_17582.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/07_2024/8pba_17582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/07_2024/8pba_17582.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/07_2024/8pba_17582.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/07_2024/8pba_17582.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/07_2024/8pba_17582.cif" } resolution = 2.64 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= 0.002 sd= 0.025 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 S 72 5.16 5 C 7410 2.51 5 N 2004 2.21 5 O 2146 1.98 5 H 11332 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A ASP 426": "OD1" <-> "OD2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "A ARG 467": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 498": "OD1" <-> "OD2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A ASP 607": "OD1" <-> "OD2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 741": "OE1" <-> "OE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 817": "OD1" <-> "OD2" Residue "A TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 891": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B ASP 426": "OD1" <-> "OD2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B ARG 467": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 498": "OD1" <-> "OD2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 572": "OE1" <-> "OE2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "B PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 615": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 636": "OE1" <-> "OE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 690": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 722": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 741": "OE1" <-> "OE2" Residue "B PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 785": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 801": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 817": "OD1" <-> "OD2" Residue "B TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 830": "OE1" <-> "OE2" Residue "B GLU 831": "OE1" <-> "OE2" Residue "B ASP 848": "OD1" <-> "OD2" Residue "B ARG 852": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 891": "OE1" <-> "OE2" 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: 22964 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11482 Classifications: {'peptide': 722} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 688} Chain breaks: 2 Chain: "B" Number of atoms: 11482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 11482 Classifications: {'peptide': 722} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 688} Chain breaks: 2 Time building chain proxies: 10.76, per 1000 atoms: 0.47 Number of scatterers: 22964 At special positions: 0 Unit cell: (97.175, 149.565, 104.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 O 2146 8.00 N 2004 7.00 C 7410 6.00 H 11332 1.00 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: 18.05 Conformation dependent library (CDL) restraints added in 2.6 seconds 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 24 sheets defined 23.1% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 44 through 60 removed outlier: 3.547A pdb=" N THR A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 301 through 307 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.630A pdb=" N TYR A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 712 through 716 removed outlier: 3.897A pdb=" N GLN A 716 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 722 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 745 through 747 No H-bonds generated for 'chain 'A' and resid 745 through 747' Processing helix chain 'A' and resid 753 through 769 Processing helix chain 'A' and resid 784 through 797 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.800A pdb=" N ARG A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 824 " --> pdb=" O TYR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 837 Processing helix chain 'A' and resid 839 through 846 removed outlier: 4.668A pdb=" N GLU A 844 " --> pdb=" O GLY A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 880 removed outlier: 3.978A pdb=" N LEU A 869 " --> pdb=" O HIS A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 917 Processing helix chain 'B' and resid 44 through 60 removed outlier: 3.537A pdb=" N THR B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 301 through 307 Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.579A pdb=" N TYR B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 712 through 716 removed outlier: 3.894A pdb=" N GLN B 716 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 745 through 747 No H-bonds generated for 'chain 'B' and resid 745 through 747' Processing helix chain 'B' and resid 753 through 769 Processing helix chain 'B' and resid 784 through 797 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.804A pdb=" N ARG B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR B 824 " --> pdb=" O TYR B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 837 Processing helix chain 'B' and resid 839 through 846 removed outlier: 4.668A pdb=" N GLU B 844 " --> pdb=" O GLY B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 880 removed outlier: 3.978A pdb=" N LEU B 869 " --> pdb=" O HIS B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 917 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.764A pdb=" N GLU A 36 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 730 " --> pdb=" O TYR A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.764A pdb=" N GLU A 36 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N LYS A 691 " --> pdb=" O MET A 773 " (cutoff:3.500A) removed outlier: 10.018A pdb=" N MET A 775 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N TYR A 693 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 777 " --> pdb=" O TYR A 693 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP A 783 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA A 803 " --> pdb=" O SER A 776 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL A 778 " --> pdb=" O ALA A 803 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE A 805 " --> pdb=" O VAL A 778 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL A 780 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLY A 807 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY A 782 " --> pdb=" O GLY A 807 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.543A pdb=" N ALA A 75 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 80 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR A 100 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 119 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 116 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 648 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 118 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR A 641 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG A 631 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR A 643 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 629 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 625 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N VAL A 649 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 14.695A pdb=" N ALA A 623 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER A 618 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR A 615 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 76 removed outlier: 3.543A pdb=" N ALA A 75 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A 80 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N THR A 100 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 119 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE A 116 " --> pdb=" O ASN A 646 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 648 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 118 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N THR A 641 " --> pdb=" O ARG A 631 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG A 631 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR A 643 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A 629 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS A 625 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N VAL A 649 " --> pdb=" O ALA A 623 " (cutoff:3.500A) removed outlier: 14.695A pdb=" N ALA A 623 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER A 618 " --> pdb=" O PRO A 622 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA A 605 " --> pdb=" O ALA A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260 removed outlier: 6.746A pdb=" N VAL A 276 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A 287 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 278 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 297 Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 398 removed outlier: 6.558A pdb=" N GLN A 408 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA A 396 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TRP A 406 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE A 398 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR A 404 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N GLN A 416 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 421 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLN A 475 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 492 through 493 removed outlier: 6.716A pdb=" N SER A 522 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR A 534 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU A 524 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AB3, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.626A pdb=" N GLU A 567 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLU A 572 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.761A pdb=" N GLU B 36 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE B 730 " --> pdb=" O TYR B 698 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.761A pdb=" N GLU B 36 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 9.508A pdb=" N LYS B 691 " --> pdb=" O MET B 773 " (cutoff:3.500A) removed outlier: 10.021A pdb=" N MET B 775 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 10.494A pdb=" N TYR B 693 " --> pdb=" O MET B 775 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 777 " --> pdb=" O TYR B 693 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TRP B 783 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ALA B 803 " --> pdb=" O SER B 776 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL B 778 " --> pdb=" O ALA B 803 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ILE B 805 " --> pdb=" O VAL B 778 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 780 " --> pdb=" O ILE B 805 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY B 807 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY B 782 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.549A pdb=" N ALA B 75 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 80 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 100 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B 119 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR B 641 " --> pdb=" O ARG B 631 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 631 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR B 643 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 629 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS B 625 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N VAL B 649 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 14.715A pdb=" N ALA B 623 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER B 618 " --> pdb=" O PRO B 622 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR B 615 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 70 through 76 removed outlier: 3.549A pdb=" N ALA B 75 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ARG B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU B 80 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR B 100 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS B 119 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR B 641 " --> pdb=" O ARG B 631 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG B 631 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N TYR B 643 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER B 629 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N CYS B 625 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N VAL B 649 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 14.715A pdb=" N ALA B 623 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER B 618 " --> pdb=" O PRO B 622 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA B 605 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 258 through 260 removed outlier: 6.744A pdb=" N VAL B 276 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG B 287 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE B 278 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AC1, first strand: chain 'B' and resid 295 through 297 Processing sheet with id=AC2, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AC3, first strand: chain 'B' and resid 390 through 398 removed outlier: 6.558A pdb=" N GLN B 408 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA B 396 " --> pdb=" O TRP B 406 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N TRP B 406 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE B 398 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR B 404 " --> pdb=" O PHE B 398 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN B 416 " --> pdb=" O SER B 411 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 421 " --> pdb=" O GLN B 475 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN B 475 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 492 through 493 removed outlier: 6.716A pdb=" N SER B 522 " --> pdb=" O THR B 534 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 534 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU B 524 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 492 through 493 Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 554 removed outlier: 4.626A pdb=" N GLU B 567 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLU B 572 " --> pdb=" O GLU B 567 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.09 Time building geometry restraints manager: 19.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 11308 1.12 - 1.29: 1914 1.29 - 1.46: 5045 1.46 - 1.64: 4879 1.64 - 1.81: 120 Bond restraints: 23266 Sorted by residual: bond pdb=" CD2 PHE B 399 " pdb=" HD2 PHE B 399 " ideal model delta sigma weight residual 0.930 1.096 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" CD2 PHE A 399 " pdb=" HD2 PHE A 399 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" NE2 HIS B 286 " pdb=" HE2 HIS B 286 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" CD1 PHE A 712 " pdb=" HD1 PHE A 712 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.78e+01 bond pdb=" CD2 PHE B 742 " pdb=" HD2 PHE B 742 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.76e+01 ... (remaining 23261 not shown) Histogram of bond angle deviations from ideal: 95.34 - 103.06: 185 103.06 - 110.78: 23550 110.78 - 118.50: 6371 118.50 - 126.21: 11504 126.21 - 133.93: 296 Bond angle restraints: 41906 Sorted by residual: angle pdb=" C ASP A 343 " pdb=" N PRO A 344 " pdb=" CA PRO A 344 " ideal model delta sigma weight residual 119.66 125.32 -5.66 7.30e-01 1.88e+00 6.00e+01 angle pdb=" C CYS A 387 " pdb=" N PRO A 388 " pdb=" CA PRO A 388 " ideal model delta sigma weight residual 119.56 127.39 -7.83 1.02e+00 9.61e-01 5.89e+01 angle pdb=" C CYS B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta sigma weight residual 119.56 127.36 -7.80 1.02e+00 9.61e-01 5.86e+01 angle pdb=" C HIS A 797 " pdb=" N PRO A 798 " pdb=" CA PRO A 798 " ideal model delta sigma weight residual 119.56 126.76 -7.20 1.01e+00 9.80e-01 5.08e+01 angle pdb=" C HIS B 797 " pdb=" N PRO B 798 " pdb=" CA PRO B 798 " ideal model delta sigma weight residual 119.56 126.72 -7.16 1.01e+00 9.80e-01 5.03e+01 ... (remaining 41901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 10336 17.10 - 34.20: 494 34.20 - 51.29: 119 51.29 - 68.39: 59 68.39 - 85.49: 12 Dihedral angle restraints: 11020 sinusoidal: 5888 harmonic: 5132 Sorted by residual: dihedral pdb=" CA TYR A 392 " pdb=" C TYR A 392 " pdb=" N ILE A 393 " pdb=" CA ILE A 393 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA TYR B 392 " pdb=" C TYR B 392 " pdb=" N ILE B 393 " pdb=" CA ILE B 393 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 429 " pdb=" C LEU A 429 " pdb=" N PRO A 430 " pdb=" CA PRO A 430 " ideal model delta harmonic sigma weight residual 180.00 160.35 19.65 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 11017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1092 0.062 - 0.124: 483 0.124 - 0.186: 111 0.186 - 0.248: 18 0.248 - 0.310: 6 Chirality restraints: 1710 Sorted by residual: chirality pdb=" CA TYR A 580 " pdb=" N TYR A 580 " pdb=" C TYR A 580 " pdb=" CB TYR A 580 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA PHE B 67 " pdb=" N PHE B 67 " pdb=" C PHE B 67 " pdb=" CB PHE B 67 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA TYR B 580 " pdb=" N TYR B 580 " pdb=" C TYR B 580 " pdb=" CB TYR B 580 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1707 not shown) Planarity restraints: 3458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 910 " 0.107 2.00e-02 2.50e+03 4.27e-02 5.48e+01 pdb=" CG TYR B 910 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR B 910 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR B 910 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR B 910 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR B 910 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR B 910 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR B 910 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TYR B 910 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR B 910 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR B 910 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 910 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 910 " -0.106 2.00e-02 2.50e+03 4.26e-02 5.46e+01 pdb=" CG TYR A 910 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 910 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 910 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR A 910 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 910 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 910 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 910 " -0.073 2.00e-02 2.50e+03 pdb=" HD1 TYR A 910 " 0.012 2.00e-02 2.50e+03 pdb=" HD2 TYR A 910 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR A 910 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR A 910 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 316 " 0.112 2.00e-02 2.50e+03 3.57e-02 5.10e+01 pdb=" CG TRP A 316 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP A 316 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 316 " -0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 316 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP A 316 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 316 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 316 " 0.021 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 316 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 316 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 TRP A 316 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP A 316 " -0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP A 316 " -0.030 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 316 " 0.044 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 316 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP A 316 " 0.024 2.00e-02 2.50e+03 ... (remaining 3455 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 403 1.94 - 2.61: 26083 2.61 - 3.27: 70176 3.27 - 3.94: 94733 3.94 - 4.60: 144903 Nonbonded interactions: 336298 Sorted by model distance: nonbonded pdb=" HG1 THR B 91 " pdb=" H ASN B 92 " model vdw 1.281 2.100 nonbonded pdb=" HG1 THR A 91 " pdb=" H ASN A 92 " model vdw 1.283 2.100 nonbonded pdb=" HG1 THR A 673 " pdb=" H LEU A 675 " model vdw 1.293 2.100 nonbonded pdb=" HH TYR A 903 " pdb="HH11 ARG A 907 " model vdw 1.443 2.100 nonbonded pdb=" HH TYR B 903 " pdb="HH11 ARG B 907 " model vdw 1.447 2.100 ... (remaining 336293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.080 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: 0.350 Extract box with map and model: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 74.240 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 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 : 0.017 0.117 11934 Z= 1.095 Angle : 1.313 7.827 16154 Z= 0.901 Chirality : 0.071 0.310 1710 Planarity : 0.011 0.056 2084 Dihedral : 11.775 85.487 4402 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.32 % Allowed : 2.31 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.95 (0.22), residues: 1432 helix: -1.95 (0.26), residues: 270 sheet: 1.43 (0.25), residues: 428 loop : 1.41 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.015 TRP A 316 HIS 0.013 0.003 HIS B 865 PHE 0.069 0.010 PHE A 40 TYR 0.097 0.015 TYR B 910 ARG 0.013 0.002 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 191 time to evaluate : 1.726 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 616 MET cc_start: 0.8212 (mmm) cc_final: 0.7928 (mmt) REVERT: B 616 MET cc_start: 0.8121 (mmm) cc_final: 0.7821 (mmt) outliers start: 4 outliers final: 0 residues processed: 195 average time/residue: 2.9832 time to fit residues: 624.9573 Evaluate side-chains 108 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN A 337 GLN ** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11934 Z= 0.198 Angle : 0.597 7.604 16154 Z= 0.327 Chirality : 0.046 0.175 1710 Planarity : 0.005 0.064 2084 Dihedral : 5.556 21.730 1594 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.75 % Allowed : 9.16 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.22), residues: 1432 helix: -0.36 (0.31), residues: 264 sheet: 0.70 (0.24), residues: 446 loop : 0.91 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 55 HIS 0.004 0.001 HIS B 677 PHE 0.024 0.002 PHE B 772 TYR 0.015 0.002 TYR A 628 ARG 0.008 0.001 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: A 616 MET cc_start: 0.8190 (mmm) cc_final: 0.7870 (mmt) REVERT: B 105 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8229 (tm) REVERT: B 616 MET cc_start: 0.8123 (mmm) cc_final: 0.7915 (mmt) outliers start: 22 outliers final: 8 residues processed: 141 average time/residue: 3.0695 time to fit residues: 465.2682 Evaluate side-chains 118 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A 669 GLN B 408 GLN B 890 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11934 Z= 0.334 Angle : 0.591 5.275 16154 Z= 0.324 Chirality : 0.046 0.166 1710 Planarity : 0.005 0.055 2084 Dihedral : 5.395 21.850 1594 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.75 % Allowed : 10.59 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.32 (0.22), residues: 1432 helix: -0.15 (0.31), residues: 262 sheet: 0.17 (0.24), residues: 454 loop : 0.59 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 55 HIS 0.005 0.001 HIS B 781 PHE 0.016 0.002 PHE A 772 TYR 0.014 0.002 TYR B 424 ARG 0.005 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 2.153 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 117 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: B 105 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8312 (tm) REVERT: B 616 MET cc_start: 0.8119 (mmm) cc_final: 0.7852 (mmt) outliers start: 22 outliers final: 13 residues processed: 134 average time/residue: 3.0186 time to fit residues: 436.4639 Evaluate side-chains 121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 482 ASP Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 848 ASP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 87 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 857 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 0.035 11934 Z= 0.241 Angle : 0.532 4.630 16154 Z= 0.288 Chirality : 0.044 0.190 1710 Planarity : 0.004 0.044 2084 Dihedral : 5.217 21.054 1594 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.99 % Allowed : 11.54 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.19 (0.22), residues: 1432 helix: -0.02 (0.31), residues: 266 sheet: -0.02 (0.24), residues: 454 loop : 0.50 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 55 HIS 0.003 0.001 HIS A 386 PHE 0.014 0.001 PHE A 772 TYR 0.011 0.002 TYR B 390 ARG 0.006 0.000 ARG B 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.787 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: A 117 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: B 105 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8379 (tm) REVERT: B 616 MET cc_start: 0.8126 (mmm) cc_final: 0.7704 (mmt) REVERT: B 680 MET cc_start: 0.8121 (ttp) cc_final: 0.7913 (ttp) outliers start: 25 outliers final: 10 residues processed: 125 average time/residue: 3.0636 time to fit residues: 411.9292 Evaluate side-chains 109 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 665 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 118 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11934 Z= 0.282 Angle : 0.537 5.569 16154 Z= 0.290 Chirality : 0.044 0.174 1710 Planarity : 0.004 0.078 2084 Dihedral : 5.158 21.260 1594 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.83 % Allowed : 11.46 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.22), residues: 1432 helix: 0.20 (0.33), residues: 254 sheet: -0.28 (0.23), residues: 456 loop : 0.30 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 55 HIS 0.005 0.001 HIS B 501 PHE 0.013 0.002 PHE A 772 TYR 0.012 0.002 TYR A 483 ARG 0.008 0.001 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.774 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: A 117 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: A 616 MET cc_start: 0.8156 (mmm) cc_final: 0.7745 (mmt) REVERT: B 35 ASN cc_start: 0.6145 (t0) cc_final: 0.5617 (m-40) REVERT: B 105 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8411 (tm) REVERT: B 616 MET cc_start: 0.8115 (mmm) cc_final: 0.7679 (mmt) outliers start: 23 outliers final: 9 residues processed: 120 average time/residue: 3.0044 time to fit residues: 388.5873 Evaluate side-chains 113 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11934 Z= 0.249 Angle : 0.518 4.832 16154 Z= 0.278 Chirality : 0.044 0.166 1710 Planarity : 0.004 0.045 2084 Dihedral : 5.067 20.631 1594 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.15 % Allowed : 11.31 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.22), residues: 1432 helix: 0.29 (0.33), residues: 254 sheet: -0.35 (0.23), residues: 456 loop : 0.20 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.004 0.001 HIS A 386 PHE 0.014 0.002 PHE A 40 TYR 0.012 0.002 TYR A 628 ARG 0.004 0.000 ARG A 892 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.644 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: A 117 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: A 616 MET cc_start: 0.8144 (mmm) cc_final: 0.7741 (mmt) REVERT: B 35 ASN cc_start: 0.6227 (t0) cc_final: 0.5934 (m-40) REVERT: B 73 MET cc_start: 0.8105 (ppp) cc_final: 0.7898 (tmm) REVERT: B 105 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8460 (tm) REVERT: B 616 MET cc_start: 0.8107 (mmm) cc_final: 0.7667 (mmt) outliers start: 27 outliers final: 11 residues processed: 124 average time/residue: 2.9677 time to fit residues: 396.3383 Evaluate side-chains 116 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN A 857 HIS ** B 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 857 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11934 Z= 0.242 Angle : 0.516 4.888 16154 Z= 0.277 Chirality : 0.044 0.163 1710 Planarity : 0.004 0.045 2084 Dihedral : 4.999 20.649 1594 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.59 % Allowed : 12.18 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.14 (0.22), residues: 1432 helix: 0.38 (0.33), residues: 254 sheet: -0.40 (0.23), residues: 452 loop : 0.12 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.003 0.001 HIS B 857 PHE 0.017 0.002 PHE B 712 TYR 0.011 0.001 TYR A 483 ARG 0.008 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 2.297 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: A 117 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: B 35 ASN cc_start: 0.6402 (t0) cc_final: 0.6119 (m-40) REVERT: B 616 MET cc_start: 0.8114 (mmm) cc_final: 0.7840 (mmt) outliers start: 20 outliers final: 10 residues processed: 125 average time/residue: 2.9652 time to fit residues: 400.5732 Evaluate side-chains 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11934 Z= 0.237 Angle : 0.515 5.709 16154 Z= 0.276 Chirality : 0.044 0.161 1710 Planarity : 0.004 0.053 2084 Dihedral : 4.971 20.468 1594 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.35 % Allowed : 12.50 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.21 (0.22), residues: 1432 helix: 0.32 (0.32), residues: 266 sheet: -0.35 (0.23), residues: 436 loop : -0.02 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 55 HIS 0.004 0.001 HIS A 386 PHE 0.017 0.001 PHE A 116 TYR 0.010 0.001 TYR A 483 ARG 0.010 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: B 35 ASN cc_start: 0.6484 (t0) cc_final: 0.6231 (m-40) REVERT: B 616 MET cc_start: 0.8073 (mmm) cc_final: 0.7798 (mmt) outliers start: 17 outliers final: 12 residues processed: 115 average time/residue: 3.0627 time to fit residues: 380.5856 Evaluate side-chains 114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 665 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 3.9990 chunk 121 optimal weight: 0.0470 chunk 129 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11934 Z= 0.159 Angle : 0.491 5.203 16154 Z= 0.260 Chirality : 0.043 0.159 1710 Planarity : 0.004 0.046 2084 Dihedral : 4.775 19.005 1594 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.19 % Allowed : 12.82 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.05 (0.22), residues: 1432 helix: 0.72 (0.34), residues: 256 sheet: -0.35 (0.24), residues: 438 loop : 0.05 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.002 0.001 HIS A 386 PHE 0.018 0.001 PHE A 116 TYR 0.010 0.001 TYR A 580 ARG 0.010 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.6557 (t0) cc_final: 0.6127 (m-40) REVERT: A 114 ARG cc_start: 0.8990 (mmm-85) cc_final: 0.8744 (tpp80) REVERT: B 35 ASN cc_start: 0.6347 (t0) cc_final: 0.6116 (m-40) REVERT: B 616 MET cc_start: 0.8055 (mmm) cc_final: 0.7779 (mmt) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 3.0477 time to fit residues: 368.9571 Evaluate side-chains 107 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 635 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11934 Z= 0.153 Angle : 0.496 6.296 16154 Z= 0.261 Chirality : 0.043 0.159 1710 Planarity : 0.004 0.046 2084 Dihedral : 4.670 18.181 1594 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.03 % Favored : 97.91 % Rotamer: Outliers : 1.27 % Allowed : 13.14 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.22), residues: 1432 helix: 0.83 (0.34), residues: 256 sheet: -0.32 (0.24), residues: 438 loop : 0.06 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 55 HIS 0.003 0.001 HIS A 386 PHE 0.016 0.001 PHE A 116 TYR 0.015 0.001 TYR A 374 ARG 0.006 0.000 ARG B 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2864 Ramachandran restraints generated. 1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.6544 (t0) cc_final: 0.6132 (m-40) REVERT: A 114 ARG cc_start: 0.8989 (mmm-85) cc_final: 0.8741 (tpp80) REVERT: A 616 MET cc_start: 0.8119 (mmm) cc_final: 0.7719 (mmt) REVERT: B 35 ASN cc_start: 0.6339 (t0) cc_final: 0.6084 (m-40) REVERT: B 616 MET cc_start: 0.8048 (mmm) cc_final: 0.7775 (mmt) outliers start: 16 outliers final: 8 residues processed: 113 average time/residue: 2.7753 time to fit residues: 342.9930 Evaluate side-chains 109 residues out of total 1256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 658 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.097052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.081362 restraints weight = 83396.168| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.45 r_work: 0.3342 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11934 Z= 0.226 Angle : 0.518 5.634 16154 Z= 0.274 Chirality : 0.043 0.157 1710 Planarity : 0.004 0.045 2084 Dihedral : 4.770 19.446 1594 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.72 % Favored : 97.21 % Rotamer: Outliers : 0.96 % Allowed : 13.69 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1432 helix: 0.72 (0.34), residues: 254 sheet: -0.34 (0.24), residues: 430 loop : 0.06 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 55 HIS 0.008 0.001 HIS A 832 PHE 0.019 0.001 PHE B 506 TYR 0.010 0.001 TYR A 483 ARG 0.006 0.000 ARG A 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8475.21 seconds wall clock time: 147 minutes 0.93 seconds (8820.93 seconds total)