Starting phenix.real_space_refine on Tue Mar 19 18:34:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu7_29454/03_2024/8fu7_29454.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu7_29454/03_2024/8fu7_29454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu7_29454/03_2024/8fu7_29454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu7_29454/03_2024/8fu7_29454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu7_29454/03_2024/8fu7_29454.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fu7_29454/03_2024/8fu7_29454.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16071 2.51 5 N 4137 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 449": not complete - not flipped Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 857": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1079": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1087": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25020 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8100 Classifications: {'peptide': 1046} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 166 Planarities with less than four sites: {'GLU:plan': 38, 'ASP:plan': 45} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8100 Classifications: {'peptide': 1046} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 166 Planarities with less than four sites: {'GLU:plan': 38, 'ASP:plan': 45} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1046, 8100 Classifications: {'peptide': 1046} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 989} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 166 Planarities with less than four sites: {'GLU:plan': 38, 'ASP:plan': 45} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 240 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 240 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 240 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Time building chain proxies: 13.12, per 1000 atoms: 0.52 Number of scatterers: 25020 At special positions: 0 Unit cell: (141.474, 135.649, 172.265, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4704 8.00 N 4137 7.00 C 16071 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: 9.61 Conformation dependent library (CDL) restraints added in 4.2 seconds 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5874 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 42 sheets defined 25.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.952A pdb=" N GLY A 175 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.896A pdb=" N ALA A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 406 Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 730 through 738 Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 742 through 767 removed outlier: 3.794A pdb=" N ASP A 759 " --> pdb=" O ALA A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 810 Processing helix chain 'A' and resid 850 through 869 Processing helix chain 'A' and resid 870 through 874 Processing helix chain 'A' and resid 881 through 892 Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.186A pdb=" N LEU A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 925 Processing helix chain 'A' and resid 929 through 949 removed outlier: 3.924A pdb=" N VAL A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 952 No H-bonds generated for 'chain 'A' and resid 950 through 952' Processing helix chain 'A' and resid 960 through 966 Processing helix chain 'A' and resid 969 through 1017 removed outlier: 4.402A pdb=" N VAL A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1130 Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.976A pdb=" N GLY B 175 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.515A pdb=" N TRP B 337 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 354 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.881A pdb=" N ALA B 395 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 406 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.588A pdb=" N VAL B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 728 Processing helix chain 'B' and resid 730 through 738 Processing helix chain 'B' and resid 739 through 741 No H-bonds generated for 'chain 'B' and resid 739 through 741' Processing helix chain 'B' and resid 742 through 767 removed outlier: 3.772A pdb=" N ASP B 759 " --> pdb=" O ALA B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 810 Processing helix chain 'B' and resid 850 through 869 Processing helix chain 'B' and resid 870 through 874 Processing helix chain 'B' and resid 881 through 892 Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.216A pdb=" N LEU B 900 " --> pdb=" O THR B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 925 Processing helix chain 'B' and resid 929 through 949 removed outlier: 3.917A pdb=" N VAL B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 960 through 966 Processing helix chain 'B' and resid 969 through 1017 removed outlier: 4.446A pdb=" N VAL B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1130 Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.967A pdb=" N GLY C 175 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.574A pdb=" N TRP C 337 " --> pdb=" O VAL C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 390 through 395 removed outlier: 3.902A pdb=" N ALA C 395 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 406 Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.593A pdb=" N VAL C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 728 Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 739 through 741 No H-bonds generated for 'chain 'C' and resid 739 through 741' Processing helix chain 'C' and resid 742 through 767 removed outlier: 3.758A pdb=" N ASP C 759 " --> pdb=" O ALA C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 810 Processing helix chain 'C' and resid 850 through 869 Processing helix chain 'C' and resid 870 through 874 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 896 through 903 removed outlier: 4.174A pdb=" N LEU C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 925 Processing helix chain 'C' and resid 929 through 949 removed outlier: 3.905A pdb=" N VAL C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 952 No H-bonds generated for 'chain 'C' and resid 950 through 952' Processing helix chain 'C' and resid 960 through 966 Processing helix chain 'C' and resid 969 through 1017 removed outlier: 4.396A pdb=" N VAL C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1130 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.680A pdb=" N ASN A 61 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR A 253 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 192 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASP A 219 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 194 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.388A pdb=" N GLY C 550 " --> pdb=" O ASP C 558 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ASP C 558 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.303A pdb=" N THR A 258 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP A 274 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 260 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 272 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS A 262 " --> pdb=" O THR A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.639A pdb=" N VAL A 130 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N PHE A 159 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 300 removed outlier: 6.933A pdb=" N VAL A 579 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 312 removed outlier: 5.763A pdb=" N ASP A 558 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY A 550 " --> pdb=" O ASP A 558 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE A 549 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 342 removed outlier: 5.527A pdb=" N ASN A 378 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU A 500 " --> pdb=" O ASN A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.515A pdb=" N CYS A 345 " --> pdb=" O CYS A 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 436 through 437 removed outlier: 4.220A pdb=" N LEU A 436 " --> pdb=" O LEU A 476 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 638 through 639 removed outlier: 6.605A pdb=" N ILE A 654 " --> pdb=" O ILE A 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 685 through 688 removed outlier: 6.503A pdb=" N ALA A 685 " --> pdb=" O ILE B 772 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS B 774 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 687 " --> pdb=" O LYS B 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 695 through 699 removed outlier: 4.252A pdb=" N PHE A1079 " --> pdb=" O ALA A1062 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 712 removed outlier: 6.019A pdb=" N TYR A1051 " --> pdb=" O HIS A1032 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS A1032 " --> pdb=" O TYR A1051 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 720 removed outlier: 4.298A pdb=" N LYS A 717 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 771 through 774 Processing sheet with id=AB7, first strand: chain 'A' and resid 1104 through 1109 removed outlier: 4.789A pdb=" N ALA A1071 " --> pdb=" O SER A1107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.904A pdb=" N ASN B 61 " --> pdb=" O TYR B 253 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N TYR B 253 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B 192 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASP B 219 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE B 194 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.227A pdb=" N THR B 258 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASP B 274 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 260 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 272 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS B 262 " --> pdb=" O THR B 270 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.971A pdb=" N GLY B 103 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 295 through 300 removed outlier: 6.932A pdb=" N VAL B 579 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 312 removed outlier: 5.843A pdb=" N ASP B 558 " --> pdb=" O ILE B 571 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY B 550 " --> pdb=" O ASP B 558 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE B 549 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 338 through 342 removed outlier: 5.529A pdb=" N ASN B 378 " --> pdb=" O GLU B 500 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 500 " --> pdb=" O ASN B 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.578A pdb=" N CYS B 345 " --> pdb=" O CYS B 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 436 through 437 removed outlier: 4.427A pdb=" N LEU B 436 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 638 through 639 removed outlier: 6.606A pdb=" N ILE B 654 " --> pdb=" O ILE B 650 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 685 through 688 removed outlier: 6.441A pdb=" N ALA B 685 " --> pdb=" O ILE C 772 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LYS C 774 " --> pdb=" O ALA B 685 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN B 687 " --> pdb=" O LYS C 774 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 695 through 712 removed outlier: 6.725A pdb=" N SER B 695 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR B1060 " --> pdb=" O SER B 695 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 697 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN B1058 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU B1056 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR B1051 " --> pdb=" O HIS B1032 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS B1032 " --> pdb=" O TYR B1051 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 695 through 712 removed outlier: 6.725A pdb=" N SER B 695 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR B1060 " --> pdb=" O SER B 695 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 697 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN B1058 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLU B1056 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE B1079 " --> pdb=" O ALA B1062 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 720 removed outlier: 4.309A pdb=" N LYS B 717 " --> pdb=" O LEU B 845 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1104 through 1109 removed outlier: 4.784A pdb=" N ALA B1071 " --> pdb=" O SER B1107 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.971A pdb=" N ASN C 61 " --> pdb=" O TYR C 253 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR C 253 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE C 192 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP C 219 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE C 194 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.231A pdb=" N THR C 258 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP C 274 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU C 260 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA C 272 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS C 262 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.000A pdb=" N GLY C 103 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 295 through 300 removed outlier: 6.931A pdb=" N VAL C 579 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 338 through 342 removed outlier: 5.521A pdb=" N ASN C 378 " --> pdb=" O GLU C 500 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 500 " --> pdb=" O ASN C 378 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.537A pdb=" N CYS C 345 " --> pdb=" O CYS C 509 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 436 through 437 removed outlier: 4.370A pdb=" N LEU C 436 " --> pdb=" O LEU C 476 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 638 through 644 removed outlier: 5.022A pdb=" N THR C 680 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN C 642 " --> pdb=" O THR C 680 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE C 654 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 695 through 712 removed outlier: 7.042A pdb=" N GLN C1055 " --> pdb=" O THR C 700 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N PHE C 702 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 704 " --> pdb=" O TYR C1051 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR C1051 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 706 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C1049 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C 708 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C1047 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 710 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C1045 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY C1043 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C1051 " --> pdb=" O HIS C1032 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N HIS C1032 " --> pdb=" O TYR C1051 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 695 through 712 removed outlier: 7.042A pdb=" N GLN C1055 " --> pdb=" O THR C 700 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N PHE C 702 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE C 704 " --> pdb=" O TYR C1051 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N TYR C1051 " --> pdb=" O ILE C 704 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL C 706 " --> pdb=" O VAL C1049 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C1049 " --> pdb=" O VAL C 706 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C 708 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU C1047 " --> pdb=" O THR C 708 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE C 710 " --> pdb=" O VAL C1045 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C1045 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY C1043 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 717 through 720 removed outlier: 4.266A pdb=" N LYS C 717 " --> pdb=" O LEU C 845 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1104 through 1109 removed outlier: 4.792A pdb=" N ALA C1071 " --> pdb=" O SER C1107 " (cutoff:3.500A) 1035 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.99 Time building geometry restraints manager: 10.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6255 1.33 - 1.46: 6524 1.46 - 1.58: 12676 1.58 - 1.71: 6 1.71 - 1.84: 138 Bond restraints: 25599 Sorted by residual: bond pdb=" C1 NAG A1211 " pdb=" O1 NAG A1211 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C1 NAG B1211 " pdb=" O1 NAG B1211 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C1 NAG A1210 " pdb=" O1 NAG A1210 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C1 NAG C1203 " pdb=" O1 NAG C1203 " ideal model delta sigma weight residual 1.376 1.482 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C1 NAG A1203 " pdb=" O1 NAG A1203 " ideal model delta sigma weight residual 1.376 1.481 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 25594 not shown) Histogram of bond angle deviations from ideal: 98.60 - 105.67: 681 105.67 - 112.75: 13520 112.75 - 119.83: 7740 119.83 - 126.91: 12637 126.91 - 133.99: 138 Bond angle restraints: 34716 Sorted by residual: angle pdb=" C LEU C 24 " pdb=" N PRO C 25 " pdb=" CA PRO C 25 " ideal model delta sigma weight residual 119.66 126.55 -6.89 7.20e-01 1.93e+00 9.16e+01 angle pdb=" C LEU B 24 " pdb=" N PRO B 25 " pdb=" CA PRO B 25 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.01e+01 angle pdb=" C LEU A 24 " pdb=" N PRO A 25 " pdb=" CA PRO A 25 " ideal model delta sigma weight residual 119.66 126.49 -6.83 7.20e-01 1.93e+00 9.00e+01 angle pdb=" C LEU C 845 " pdb=" N PRO C 846 " pdb=" CA PRO C 846 " ideal model delta sigma weight residual 119.66 125.17 -5.51 7.20e-01 1.93e+00 5.86e+01 angle pdb=" C LEU A 845 " pdb=" N PRO A 846 " pdb=" CA PRO A 846 " ideal model delta sigma weight residual 119.66 125.08 -5.42 7.20e-01 1.93e+00 5.67e+01 ... (remaining 34711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.53: 15552 20.53 - 41.06: 365 41.06 - 61.60: 86 61.60 - 82.13: 28 82.13 - 102.66: 7 Dihedral angle restraints: 16038 sinusoidal: 6903 harmonic: 9135 Sorted by residual: dihedral pdb=" CB GLU B 449 " pdb=" CG GLU B 449 " pdb=" CD GLU B 449 " pdb=" OE1 GLU B 449 " ideal model delta sinusoidal sigma weight residual 0.00 102.66 -102.66 1 3.00e+01 1.11e-03 1.30e+01 dihedral pdb=" CA GLN B 490 " pdb=" C GLN B 490 " pdb=" N PRO B 491 " pdb=" CA PRO B 491 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA GLN A 490 " pdb=" C GLN A 490 " pdb=" N PRO A 491 " pdb=" CA PRO A 491 " ideal model delta harmonic sigma weight residual 180.00 162.52 17.48 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 16035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3194 0.084 - 0.168: 689 0.168 - 0.252: 130 0.252 - 0.335: 96 0.335 - 0.419: 4 Chirality restraints: 4113 Sorted by residual: chirality pdb=" CA ALA C 877 " pdb=" N ALA C 877 " pdb=" C ALA C 877 " pdb=" CB ALA C 877 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CG LEU A 24 " pdb=" CB LEU A 24 " pdb=" CD1 LEU A 24 " pdb=" CD2 LEU A 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CG LEU C 24 " pdb=" CB LEU C 24 " pdb=" CD1 LEU C 24 " pdb=" CD2 LEU C 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 4110 not shown) Planarity restraints: 4239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 437 " -0.038 2.00e-02 2.50e+03 2.14e-02 9.12e+00 pdb=" CG TYR B 437 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR B 437 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 437 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 437 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 437 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR B 437 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 437 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 437 " -0.032 2.00e-02 2.50e+03 1.81e-02 6.52e+00 pdb=" CG TYR C 437 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR C 437 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 437 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR C 437 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR C 437 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR C 437 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 437 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1204 " -0.025 2.00e-02 2.50e+03 2.05e-02 5.23e+00 pdb=" C7 NAG A1204 " 0.004 2.00e-02 2.50e+03 pdb=" C8 NAG A1204 " -0.019 2.00e-02 2.50e+03 pdb=" N2 NAG A1204 " 0.032 2.00e-02 2.50e+03 pdb=" O7 NAG A1204 " 0.007 2.00e-02 2.50e+03 ... (remaining 4236 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1164 2.71 - 3.26: 24679 3.26 - 3.80: 39718 3.80 - 4.35: 51846 4.35 - 4.90: 86225 Nonbonded interactions: 203632 Sorted by model distance: nonbonded pdb=" ND2 ASN B 378 " pdb=" OH TYR C 191 " model vdw 2.159 2.520 nonbonded pdb=" OH TYR A 191 " pdb=" ND2 ASN C 378 " model vdw 2.171 2.520 nonbonded pdb=" ND2 ASN A 378 " pdb=" OH TYR B 191 " model vdw 2.175 2.520 nonbonded pdb=" O LEU C 277 " pdb=" OG1 THR C 616 " model vdw 2.338 2.440 nonbonded pdb=" O LEU B 277 " pdb=" OG1 THR B 616 " model vdw 2.352 2.440 ... (remaining 203627 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' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.740 Check model and map are aligned: 0.460 Set scattering table: 0.210 Process input model: 68.890 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.130 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.012 0.106 25599 Z= 0.825 Angle : 1.297 9.070 34716 Z= 0.875 Chirality : 0.082 0.419 4113 Planarity : 0.005 0.029 4239 Dihedral : 10.159 102.659 10164 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.87 % Allowed : 5.18 % Favored : 93.95 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.35 (0.14), residues: 3108 helix: 0.50 (0.18), residues: 663 sheet: 1.05 (0.20), residues: 570 loop : -0.95 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP C 64 HIS 0.004 0.001 HIS A 137 PHE 0.025 0.003 PHE A 474 TYR 0.038 0.005 TYR B 437 ARG 0.003 0.000 ARG A 984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 490 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ASN cc_start: 0.6990 (m-40) cc_final: 0.6762 (t0) REVERT: A 319 LEU cc_start: 0.6677 (mt) cc_final: 0.6216 (tp) REVERT: A 344 ASN cc_start: 0.8066 (m-40) cc_final: 0.7841 (m-40) REVERT: A 352 LEU cc_start: 0.8499 (mt) cc_final: 0.8220 (mp) REVERT: A 360 THR cc_start: 0.6356 (t) cc_final: 0.6143 (p) REVERT: A 378 ASN cc_start: 0.6430 (m-40) cc_final: 0.6059 (m-40) REVERT: A 380 TYR cc_start: 0.6967 (m-80) cc_final: 0.6718 (m-80) REVERT: A 392 ARG cc_start: 0.7719 (ptt90) cc_final: 0.7426 (ppt170) REVERT: A 405 TYR cc_start: 0.7580 (m-80) cc_final: 0.6997 (m-80) REVERT: A 408 LYS cc_start: 0.6716 (tttp) cc_final: 0.6494 (tptp) REVERT: A 497 LEU cc_start: 0.8464 (mt) cc_final: 0.8256 (mp) REVERT: A 498 SER cc_start: 0.8000 (t) cc_final: 0.7576 (p) REVERT: A 625 ASN cc_start: 0.6984 (m-40) cc_final: 0.6469 (p0) REVERT: A 919 GLN cc_start: 0.6964 (mt0) cc_final: 0.6635 (mt0) REVERT: B 121 ASN cc_start: 0.7042 (m-40) cc_final: 0.6782 (t0) REVERT: B 196 SER cc_start: 0.9012 (p) cc_final: 0.8597 (m) REVERT: B 340 LYS cc_start: 0.7411 (tttp) cc_final: 0.7161 (tttt) REVERT: B 344 ASN cc_start: 0.8117 (m-40) cc_final: 0.7904 (m-40) REVERT: B 352 LEU cc_start: 0.8552 (mt) cc_final: 0.8332 (mp) REVERT: B 378 ASN cc_start: 0.6508 (m-40) cc_final: 0.6306 (m-40) REVERT: B 380 TYR cc_start: 0.7171 (m-80) cc_final: 0.6796 (m-80) REVERT: B 393 GLN cc_start: 0.7661 (mt0) cc_final: 0.7335 (tt0) REVERT: B 405 TYR cc_start: 0.7546 (m-80) cc_final: 0.6917 (m-80) REVERT: B 408 LYS cc_start: 0.6680 (tttp) cc_final: 0.6344 (tptp) REVERT: B 498 SER cc_start: 0.7880 (t) cc_final: 0.7483 (p) REVERT: B 625 ASN cc_start: 0.7074 (m-40) cc_final: 0.6510 (p0) REVERT: B 919 GLN cc_start: 0.7179 (mt0) cc_final: 0.6966 (mt0) REVERT: C 28 TYR cc_start: 0.3827 (m-80) cc_final: 0.3564 (m-80) REVERT: C 105 ILE cc_start: 0.7899 (mt) cc_final: 0.7638 (mm) REVERT: C 310 ILE cc_start: 0.7440 (mt) cc_final: 0.7213 (pt) REVERT: C 319 LEU cc_start: 0.6525 (mt) cc_final: 0.6155 (tp) REVERT: C 344 ASN cc_start: 0.8088 (m-40) cc_final: 0.7804 (m-40) REVERT: C 380 TYR cc_start: 0.7016 (m-80) cc_final: 0.6451 (m-80) REVERT: C 392 ARG cc_start: 0.7745 (ptt90) cc_final: 0.7532 (ppt170) REVERT: C 408 LYS cc_start: 0.6845 (tttp) cc_final: 0.6470 (tptp) REVERT: C 498 SER cc_start: 0.8021 (t) cc_final: 0.7589 (p) REVERT: C 674 GLN cc_start: 0.4243 (mp10) cc_final: 0.3614 (mt0) REVERT: C 888 TYR cc_start: 0.7380 (m-10) cc_final: 0.7004 (m-10) outliers start: 2 outliers final: 0 residues processed: 492 average time/residue: 0.3929 time to fit residues: 293.0242 Evaluate side-chains 274 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 1.9990 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 0.5980 chunk 283 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 315 ASN A 587 ASN A 693 ASN B 198 HIS B 315 ASN B 587 ASN B 701 ASN B 748 ASN C 121 ASN C 315 ASN C 587 ASN C 701 ASN C 748 ASN C 897 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25599 Z= 0.202 Angle : 0.605 8.065 34716 Z= 0.326 Chirality : 0.046 0.229 4113 Planarity : 0.005 0.046 4239 Dihedral : 5.393 50.667 4515 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.21 % Favored : 93.60 % Rotamer: Outliers : 1.42 % Allowed : 4.66 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.15), residues: 3108 helix: 1.81 (0.21), residues: 669 sheet: 1.27 (0.20), residues: 591 loop : -1.18 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 420 HIS 0.023 0.001 HIS A 137 PHE 0.030 0.002 PHE B 135 TYR 0.023 0.001 TYR B 161 ARG 0.007 0.001 ARG C 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 324 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 SER cc_start: 0.8697 (p) cc_final: 0.8421 (m) REVERT: A 319 LEU cc_start: 0.6587 (mt) cc_final: 0.6186 (tp) REVERT: A 340 LYS cc_start: 0.7446 (tttp) cc_final: 0.7138 (tttt) REVERT: A 349 TYR cc_start: 0.8123 (m-80) cc_final: 0.7579 (m-80) REVERT: A 385 VAL cc_start: 0.5272 (t) cc_final: 0.5031 (m) REVERT: A 405 TYR cc_start: 0.7456 (m-80) cc_final: 0.6844 (m-80) REVERT: A 498 SER cc_start: 0.7808 (t) cc_final: 0.7550 (p) REVERT: B 181 ARG cc_start: 0.7743 (mtm-85) cc_final: 0.7522 (mtm-85) REVERT: B 196 SER cc_start: 0.8757 (p) cc_final: 0.8493 (m) REVERT: B 340 LYS cc_start: 0.7573 (tttp) cc_final: 0.7292 (tttt) REVERT: B 405 TYR cc_start: 0.7617 (m-80) cc_final: 0.6997 (m-80) REVERT: B 408 LYS cc_start: 0.6798 (tttp) cc_final: 0.6561 (tptp) REVERT: B 493 ARG cc_start: 0.4304 (mtp85) cc_final: 0.4053 (mmt90) REVERT: B 498 SER cc_start: 0.7908 (t) cc_final: 0.7595 (p) REVERT: B 568 ILE cc_start: 0.8239 (mm) cc_final: 0.7994 (pt) REVERT: B 891 ASN cc_start: 0.8360 (t0) cc_final: 0.8064 (t0) REVERT: C 105 ILE cc_start: 0.7862 (mt) cc_final: 0.7649 (mm) REVERT: C 125 ASN cc_start: 0.6839 (m-40) cc_final: 0.6594 (m-40) REVERT: C 196 SER cc_start: 0.8732 (p) cc_final: 0.8426 (m) REVERT: C 319 LEU cc_start: 0.6613 (mt) cc_final: 0.6313 (tp) REVERT: C 340 LYS cc_start: 0.7778 (tttp) cc_final: 0.7463 (tttt) REVERT: C 408 LYS cc_start: 0.6933 (tttp) cc_final: 0.6640 (tptp) REVERT: C 498 SER cc_start: 0.7786 (t) cc_final: 0.7387 (p) REVERT: C 674 GLN cc_start: 0.4385 (mp10) cc_final: 0.3957 (mt0) outliers start: 39 outliers final: 24 residues processed: 352 average time/residue: 0.3374 time to fit residues: 193.1139 Evaluate side-chains 270 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 246 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 283 optimal weight: 0.0040 chunk 306 optimal weight: 0.9980 chunk 252 optimal weight: 3.9990 chunk 281 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN B 121 ASN B 587 ASN ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 HIS C 587 ASN C 919 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25599 Z= 0.160 Angle : 0.542 7.539 34716 Z= 0.290 Chirality : 0.043 0.184 4113 Planarity : 0.004 0.054 4239 Dihedral : 4.935 45.673 4515 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.76 % Favored : 93.18 % Rotamer: Outliers : 1.42 % Allowed : 6.11 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3108 helix: 2.09 (0.21), residues: 669 sheet: 0.95 (0.20), residues: 642 loop : -1.24 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1086 HIS 0.016 0.001 HIS A 137 PHE 0.019 0.001 PHE A 474 TYR 0.026 0.001 TYR A 161 ARG 0.007 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 272 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7220 (m-80) cc_final: 0.6827 (m-80) REVERT: A 196 SER cc_start: 0.8783 (p) cc_final: 0.8563 (m) REVERT: A 319 LEU cc_start: 0.6568 (mt) cc_final: 0.6182 (tp) REVERT: A 340 LYS cc_start: 0.7449 (tttp) cc_final: 0.7186 (tttt) REVERT: A 385 VAL cc_start: 0.5262 (t) cc_final: 0.5018 (m) REVERT: A 498 SER cc_start: 0.7784 (t) cc_final: 0.7476 (p) REVERT: B 340 LYS cc_start: 0.7506 (tttp) cc_final: 0.7264 (tttt) REVERT: B 408 LYS cc_start: 0.6831 (tttp) cc_final: 0.6613 (tptp) REVERT: B 448 PHE cc_start: 0.7045 (m-10) cc_final: 0.6624 (m-80) REVERT: B 498 SER cc_start: 0.7840 (t) cc_final: 0.7462 (p) REVERT: B 891 ASN cc_start: 0.8300 (t0) cc_final: 0.7988 (t0) REVERT: C 105 ILE cc_start: 0.7958 (mt) cc_final: 0.7745 (mm) REVERT: C 125 ASN cc_start: 0.6831 (m-40) cc_final: 0.6594 (m-40) REVERT: C 191 TYR cc_start: 0.7247 (m-80) cc_final: 0.6949 (m-10) REVERT: C 196 SER cc_start: 0.8756 (p) cc_final: 0.8518 (m) REVERT: C 319 LEU cc_start: 0.6637 (mt) cc_final: 0.6328 (tp) REVERT: C 340 LYS cc_start: 0.7750 (tttp) cc_final: 0.7437 (tttt) REVERT: C 408 LYS cc_start: 0.6957 (tttp) cc_final: 0.6647 (tptp) REVERT: C 448 PHE cc_start: 0.7009 (m-10) cc_final: 0.6384 (m-80) REVERT: C 498 SER cc_start: 0.7787 (t) cc_final: 0.7380 (p) REVERT: C 674 GLN cc_start: 0.4137 (mp10) cc_final: 0.3670 (mt0) outliers start: 39 outliers final: 27 residues processed: 300 average time/residue: 0.3316 time to fit residues: 164.0123 Evaluate side-chains 272 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 245 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 1034 MET Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 884 MET Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 788 GLN Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 147 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 284 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 393 GLN A 587 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1032 HIS B 639 HIS B 701 ASN C 140 ASN C 230 GLN C 393 GLN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 ASN ** C 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1032 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25599 Z= 0.269 Angle : 0.587 7.593 34716 Z= 0.311 Chirality : 0.045 0.205 4113 Planarity : 0.005 0.052 4239 Dihedral : 5.167 39.057 4515 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.92 % Favored : 93.02 % Rotamer: Outliers : 2.26 % Allowed : 6.66 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.30 (0.15), residues: 3108 helix: 1.86 (0.21), residues: 672 sheet: 0.77 (0.20), residues: 615 loop : -1.43 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 870 HIS 0.012 0.001 HIS A 137 PHE 0.018 0.002 PHE A 474 TYR 0.022 0.002 TYR B1051 ARG 0.006 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 263 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7272 (m-80) cc_final: 0.6896 (m-80) REVERT: A 319 LEU cc_start: 0.6420 (mt) cc_final: 0.6195 (tt) REVERT: A 340 LYS cc_start: 0.7532 (tttp) cc_final: 0.7163 (tttt) REVERT: A 498 SER cc_start: 0.7781 (t) cc_final: 0.7426 (p) REVERT: A 576 PHE cc_start: 0.7927 (p90) cc_final: 0.7687 (p90) REVERT: A 587 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7415 (t160) REVERT: B 48 LEU cc_start: 0.8646 (mt) cc_final: 0.8442 (mp) REVERT: B 181 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7345 (mtm-85) REVERT: B 340 LYS cc_start: 0.7477 (tttp) cc_final: 0.7186 (tttt) REVERT: B 380 TYR cc_start: 0.7028 (m-80) cc_final: 0.6758 (m-80) REVERT: B 405 TYR cc_start: 0.7556 (m-80) cc_final: 0.7004 (m-80) REVERT: B 409 LEU cc_start: 0.7427 (mt) cc_final: 0.7198 (mp) REVERT: B 498 SER cc_start: 0.7811 (t) cc_final: 0.7455 (p) REVERT: B 891 ASN cc_start: 0.8381 (t0) cc_final: 0.8018 (t0) REVERT: C 48 LEU cc_start: 0.8540 (mt) cc_final: 0.8286 (mp) REVERT: C 58 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8148 (m-10) REVERT: C 181 ARG cc_start: 0.7669 (mtm-85) cc_final: 0.7447 (mtm-85) REVERT: C 191 TYR cc_start: 0.7370 (m-80) cc_final: 0.7140 (m-10) REVERT: C 319 LEU cc_start: 0.6439 (mt) cc_final: 0.6173 (tp) REVERT: C 362 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7877 (ptmt) REVERT: C 405 TYR cc_start: 0.7224 (m-80) cc_final: 0.6970 (m-10) REVERT: C 408 LYS cc_start: 0.7072 (tttp) cc_final: 0.6759 (tptp) REVERT: C 498 SER cc_start: 0.7799 (t) cc_final: 0.7359 (p) REVERT: C 674 GLN cc_start: 0.4211 (mp10) cc_final: 0.3694 (mt0) outliers start: 62 outliers final: 39 residues processed: 311 average time/residue: 0.3318 time to fit residues: 167.6524 Evaluate side-chains 279 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 238 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 587 ASN Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 701 ASN Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 775 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 270 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B1118 ASN ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN C 490 GLN C 587 ASN C 639 HIS C1118 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 25599 Z= 0.401 Angle : 0.650 9.548 34716 Z= 0.345 Chirality : 0.047 0.232 4113 Planarity : 0.005 0.053 4239 Dihedral : 5.802 43.739 4515 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 2.40 % Allowed : 7.79 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.71 (0.15), residues: 3108 helix: 1.79 (0.21), residues: 642 sheet: 0.54 (0.21), residues: 579 loop : -1.73 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 870 HIS 0.010 0.001 HIS A 137 PHE 0.026 0.002 PHE B 474 TYR 0.024 0.002 TYR B1051 ARG 0.006 0.001 ARG C 998 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7277 (m-80) cc_final: 0.6954 (m-80) REVERT: A 121 ASN cc_start: 0.6935 (OUTLIER) cc_final: 0.6117 (m-40) REVERT: A 319 LEU cc_start: 0.6349 (mt) cc_final: 0.6106 (tt) REVERT: A 345 CYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7688 (p) REVERT: A 362 LYS cc_start: 0.7620 (tptt) cc_final: 0.7323 (ttmt) REVERT: A 498 SER cc_start: 0.7769 (t) cc_final: 0.7388 (p) REVERT: A 576 PHE cc_start: 0.7835 (p90) cc_final: 0.7541 (p90) REVERT: B 181 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7294 (mtm-85) REVERT: B 212 SER cc_start: 0.8472 (m) cc_final: 0.8185 (p) REVERT: B 362 LYS cc_start: 0.8066 (ttpt) cc_final: 0.7751 (ptmt) REVERT: B 380 TYR cc_start: 0.7168 (m-80) cc_final: 0.6883 (m-80) REVERT: B 498 SER cc_start: 0.7863 (t) cc_final: 0.7530 (p) REVERT: B 891 ASN cc_start: 0.8405 (t0) cc_final: 0.8025 (t0) REVERT: C 58 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.8190 (m-10) REVERT: C 319 LEU cc_start: 0.6360 (mt) cc_final: 0.6092 (tt) REVERT: C 345 CYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7312 (p) REVERT: C 362 LYS cc_start: 0.8201 (ttpt) cc_final: 0.7885 (ptmt) REVERT: C 405 TYR cc_start: 0.7096 (m-80) cc_final: 0.6858 (m-10) REVERT: C 408 LYS cc_start: 0.7047 (tttp) cc_final: 0.6784 (tptp) REVERT: C 498 SER cc_start: 0.7805 (t) cc_final: 0.7384 (p) REVERT: C 674 GLN cc_start: 0.4161 (mp10) cc_final: 0.3645 (mt0) outliers start: 66 outliers final: 46 residues processed: 294 average time/residue: 0.3212 time to fit residues: 156.2944 Evaluate side-chains 267 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 217 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25599 Z= 0.169 Angle : 0.539 8.583 34716 Z= 0.287 Chirality : 0.043 0.179 4113 Planarity : 0.004 0.060 4239 Dihedral : 5.145 43.008 4515 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.50 % Favored : 92.44 % Rotamer: Outliers : 1.71 % Allowed : 8.95 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.53 (0.15), residues: 3108 helix: 1.81 (0.21), residues: 678 sheet: 0.62 (0.20), residues: 606 loop : -1.66 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1086 HIS 0.008 0.001 HIS A 137 PHE 0.023 0.001 PHE B 474 TYR 0.020 0.001 TYR B 161 ARG 0.008 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 246 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7231 (m-80) cc_final: 0.6971 (m-80) REVERT: A 319 LEU cc_start: 0.6318 (mt) cc_final: 0.6115 (tt) REVERT: A 413 PHE cc_start: 0.6882 (t80) cc_final: 0.6487 (t80) REVERT: A 498 SER cc_start: 0.7848 (t) cc_final: 0.7523 (p) REVERT: A 576 PHE cc_start: 0.7867 (p90) cc_final: 0.7630 (p90) REVERT: B 64 TRP cc_start: 0.7473 (t60) cc_final: 0.7205 (t60) REVERT: B 212 SER cc_start: 0.8453 (m) cc_final: 0.8181 (p) REVERT: B 345 CYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7322 (p) REVERT: B 362 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7793 (ptmt) REVERT: B 380 TYR cc_start: 0.7159 (m-80) cc_final: 0.6956 (m-80) REVERT: B 448 PHE cc_start: 0.7031 (m-10) cc_final: 0.6696 (m-80) REVERT: B 498 SER cc_start: 0.7854 (t) cc_final: 0.7494 (p) REVERT: B 891 ASN cc_start: 0.8318 (t0) cc_final: 0.7971 (t0) REVERT: C 58 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7869 (m-10) REVERT: C 181 ARG cc_start: 0.7816 (mtm-85) cc_final: 0.7595 (mtm-85) REVERT: C 362 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7779 (ptmt) REVERT: C 405 TYR cc_start: 0.7175 (m-80) cc_final: 0.6882 (m-10) REVERT: C 408 LYS cc_start: 0.7177 (tttp) cc_final: 0.6924 (tptp) REVERT: C 448 PHE cc_start: 0.6874 (m-80) cc_final: 0.6613 (m-80) REVERT: C 498 SER cc_start: 0.7803 (t) cc_final: 0.7405 (p) REVERT: C 674 GLN cc_start: 0.4134 (mp10) cc_final: 0.3602 (mt0) outliers start: 47 outliers final: 34 residues processed: 282 average time/residue: 0.3660 time to fit residues: 169.4987 Evaluate side-chains 263 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.1980 chunk 34 optimal weight: 4.9990 chunk 171 optimal weight: 0.0770 chunk 220 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 300 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN B 209 GLN B 482 GLN ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25599 Z= 0.182 Angle : 0.540 8.835 34716 Z= 0.285 Chirality : 0.043 0.266 4113 Planarity : 0.004 0.066 4239 Dihedral : 4.917 38.077 4515 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.34 % Rotamer: Outliers : 2.00 % Allowed : 9.10 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.52 (0.15), residues: 3108 helix: 1.89 (0.21), residues: 681 sheet: 0.55 (0.21), residues: 588 loop : -1.63 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 420 HIS 0.008 0.001 HIS A 137 PHE 0.021 0.001 PHE B 376 TYR 0.020 0.001 TYR B1051 ARG 0.005 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 235 time to evaluate : 2.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7267 (m-80) cc_final: 0.7004 (m-80) REVERT: A 319 LEU cc_start: 0.6330 (mt) cc_final: 0.6051 (tt) REVERT: A 345 CYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7486 (p) REVERT: A 498 SER cc_start: 0.7831 (t) cc_final: 0.7525 (p) REVERT: A 576 PHE cc_start: 0.7803 (p90) cc_final: 0.7554 (p90) REVERT: B 64 TRP cc_start: 0.7482 (t60) cc_final: 0.7200 (t60) REVERT: B 212 SER cc_start: 0.8428 (m) cc_final: 0.8169 (p) REVERT: B 345 CYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7209 (p) REVERT: B 362 LYS cc_start: 0.8051 (ttpt) cc_final: 0.7799 (ptmt) REVERT: B 448 PHE cc_start: 0.6888 (m-10) cc_final: 0.6588 (m-80) REVERT: B 498 SER cc_start: 0.7896 (t) cc_final: 0.7516 (p) REVERT: B 891 ASN cc_start: 0.8313 (t0) cc_final: 0.7982 (t0) REVERT: C 58 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7816 (m-10) REVERT: C 181 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7568 (mtm-85) REVERT: C 319 LEU cc_start: 0.7257 (tp) cc_final: 0.6954 (tp) REVERT: C 345 CYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7114 (p) REVERT: C 362 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7805 (ptmt) REVERT: C 405 TYR cc_start: 0.7150 (m-80) cc_final: 0.6864 (m-10) REVERT: C 408 LYS cc_start: 0.7180 (tttp) cc_final: 0.6949 (tptp) REVERT: C 448 PHE cc_start: 0.6909 (m-80) cc_final: 0.6323 (m-80) REVERT: C 498 SER cc_start: 0.7795 (t) cc_final: 0.7357 (p) outliers start: 55 outliers final: 43 residues processed: 276 average time/residue: 0.3235 time to fit residues: 146.3472 Evaluate side-chains 270 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 223 time to evaluate : 2.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 9.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 639 HIS ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 GLN C 587 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 25599 Z= 0.396 Angle : 0.658 9.495 34716 Z= 0.347 Chirality : 0.047 0.218 4113 Planarity : 0.005 0.067 4239 Dihedral : 5.867 46.723 4515 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.30 % Favored : 91.57 % Rotamer: Outliers : 2.26 % Allowed : 9.21 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.96 (0.15), residues: 3108 helix: 1.57 (0.21), residues: 663 sheet: 0.34 (0.21), residues: 570 loop : -1.90 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 870 HIS 0.008 0.001 HIS A 137 PHE 0.028 0.002 PHE B 474 TYR 0.025 0.002 TYR A 888 ARG 0.007 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 213 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LEU cc_start: 0.6352 (mt) cc_final: 0.6136 (tt) REVERT: A 345 CYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7493 (p) REVERT: A 362 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7758 (ptmt) REVERT: A 498 SER cc_start: 0.7769 (t) cc_final: 0.7398 (p) REVERT: A 576 PHE cc_start: 0.7849 (p90) cc_final: 0.7536 (p90) REVERT: B 64 TRP cc_start: 0.7581 (t60) cc_final: 0.7373 (t60) REVERT: B 212 SER cc_start: 0.8380 (m) cc_final: 0.8115 (p) REVERT: B 345 CYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7326 (p) REVERT: B 362 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7816 (ptmt) REVERT: B 498 SER cc_start: 0.7915 (t) cc_final: 0.7555 (p) REVERT: B 891 ASN cc_start: 0.8387 (t0) cc_final: 0.7977 (t0) REVERT: C 32 PHE cc_start: 0.7196 (m-80) cc_final: 0.6967 (m-80) REVERT: C 58 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8076 (m-10) REVERT: C 319 LEU cc_start: 0.7176 (tp) cc_final: 0.6904 (tp) REVERT: C 345 CYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7318 (p) REVERT: C 405 TYR cc_start: 0.7161 (m-80) cc_final: 0.6916 (m-10) REVERT: C 498 SER cc_start: 0.7832 (t) cc_final: 0.7409 (p) outliers start: 62 outliers final: 48 residues processed: 266 average time/residue: 0.3451 time to fit residues: 152.8149 Evaluate side-chains 259 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 318 ASN Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 775 THR Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 318 ASN Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 549 PHE Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.7980 chunk 288 optimal weight: 0.8980 chunk 262 optimal weight: 3.9990 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 122 optimal weight: 0.1980 chunk 220 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 253 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 279 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 ASN ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 25599 Z= 0.162 Angle : 0.535 8.576 34716 Z= 0.284 Chirality : 0.043 0.182 4113 Planarity : 0.005 0.084 4239 Dihedral : 5.001 40.883 4515 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 1.60 % Allowed : 9.90 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.65 (0.15), residues: 3108 helix: 1.84 (0.21), residues: 678 sheet: 0.47 (0.21), residues: 603 loop : -1.76 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 143 HIS 0.007 0.001 HIS A 137 PHE 0.025 0.001 PHE B 474 TYR 0.021 0.001 TYR B1051 ARG 0.007 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 231 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7225 (m-80) cc_final: 0.6981 (m-80) REVERT: A 319 LEU cc_start: 0.6314 (mt) cc_final: 0.6101 (tt) REVERT: A 345 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7485 (p) REVERT: A 362 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7724 (ptmt) REVERT: A 498 SER cc_start: 0.7846 (t) cc_final: 0.7544 (p) REVERT: A 576 PHE cc_start: 0.7759 (p90) cc_final: 0.7449 (p90) REVERT: B 64 TRP cc_start: 0.7438 (t60) cc_final: 0.7203 (t60) REVERT: B 212 SER cc_start: 0.8358 (m) cc_final: 0.8125 (p) REVERT: B 345 CYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7147 (p) REVERT: B 362 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7760 (ptmt) REVERT: B 498 SER cc_start: 0.7843 (t) cc_final: 0.7531 (p) REVERT: B 891 ASN cc_start: 0.8294 (t0) cc_final: 0.7947 (t0) REVERT: C 58 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7696 (m-10) REVERT: C 345 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7212 (p) REVERT: C 362 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7873 (ptmt) REVERT: C 498 SER cc_start: 0.7698 (t) cc_final: 0.7303 (p) outliers start: 44 outliers final: 33 residues processed: 264 average time/residue: 0.3499 time to fit residues: 154.2541 Evaluate side-chains 258 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 221 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 205 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 25599 Z= 0.260 Angle : 0.682 59.198 34716 Z= 0.383 Chirality : 0.045 0.256 4113 Planarity : 0.005 0.079 4239 Dihedral : 5.002 40.838 4515 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.04 % Favored : 91.83 % Rotamer: Outliers : 1.56 % Allowed : 10.01 % Favored : 88.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.66 (0.15), residues: 3108 helix: 1.84 (0.21), residues: 678 sheet: 0.49 (0.21), residues: 603 loop : -1.77 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 143 HIS 0.007 0.001 HIS A 137 PHE 0.024 0.002 PHE B 474 TYR 0.036 0.001 TYR C 492 ARG 0.008 0.000 ARG C 181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6216 Ramachandran restraints generated. 3108 Oldfield, 0 Emsley, 3108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 222 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7230 (m-80) cc_final: 0.6987 (m-80) REVERT: A 319 LEU cc_start: 0.6314 (mt) cc_final: 0.6104 (tt) REVERT: A 345 CYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7488 (p) REVERT: A 362 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7744 (ptmt) REVERT: A 498 SER cc_start: 0.7836 (t) cc_final: 0.7544 (p) REVERT: A 576 PHE cc_start: 0.7760 (p90) cc_final: 0.7452 (p90) REVERT: B 64 TRP cc_start: 0.7446 (t60) cc_final: 0.7207 (t60) REVERT: B 212 SER cc_start: 0.8358 (m) cc_final: 0.8125 (p) REVERT: B 345 CYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7143 (p) REVERT: B 362 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7764 (ptmt) REVERT: B 498 SER cc_start: 0.7833 (t) cc_final: 0.7534 (p) REVERT: B 891 ASN cc_start: 0.8302 (t0) cc_final: 0.7958 (t0) REVERT: C 58 PHE cc_start: 0.8250 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: C 345 CYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7214 (p) REVERT: C 362 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7879 (ptmt) REVERT: C 405 TYR cc_start: 0.6814 (m-80) cc_final: 0.6284 (m-10) REVERT: C 498 SER cc_start: 0.7689 (t) cc_final: 0.7302 (p) outliers start: 43 outliers final: 36 residues processed: 252 average time/residue: 0.3206 time to fit residues: 133.8846 Evaluate side-chains 262 residues out of total 2748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 222 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 345 CYS Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 549 PHE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 788 GLN Chi-restraints excluded: chain A residue 1082 ASN Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 897 GLN Chi-restraints excluded: chain B residue 900 LEU Chi-restraints excluded: chain B residue 1034 MET Chi-restraints excluded: chain B residue 1082 ASN Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 345 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 617 TRP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 977 ILE Chi-restraints excluded: chain C residue 1082 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 75 optimal weight: 8.9990 chunk 228 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 0.0270 chunk 103 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 31 optimal weight: 0.2980 chunk 45 optimal weight: 0.3980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116137 restraints weight = 39127.255| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.11 r_work: 0.3153 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 25599 Z= 0.260 Angle : 0.682 59.198 34716 Z= 0.383 Chirality : 0.045 0.256 4113 Planarity : 0.005 0.083 4239 Dihedral : 5.002 40.838 4515 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.04 % Favored : 91.83 % Rotamer: Outliers : 1.46 % Allowed : 10.12 % Favored : 88.43 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.66 (0.15), residues: 3108 helix: 1.84 (0.21), residues: 678 sheet: 0.49 (0.21), residues: 603 loop : -1.77 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 143 HIS 0.007 0.001 HIS A 137 PHE 0.024 0.002 PHE B 474 TYR 0.036 0.001 TYR C 492 ARG 0.008 0.000 ARG C 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5318.64 seconds wall clock time: 97 minutes 43.78 seconds (5863.78 seconds total)