Starting phenix.real_space_refine on Tue Mar 19 18:20:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/03_2024/7vhm_31999.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/03_2024/7vhm_31999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/03_2024/7vhm_31999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/03_2024/7vhm_31999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/03_2024/7vhm_31999.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/03_2024/7vhm_31999.pdb" } resolution = 3.2 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= 0.004 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 117 5.16 5 C 15966 2.51 5 N 4149 2.21 5 O 4740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 759": "OD1" <-> "OD2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A ASP 934": "OD1" <-> "OD2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1056": "OE1" <-> "OE2" Residue "A PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1102": "OD1" <-> "OD2" Residue "A ASP 1111": "OD1" <-> "OD2" Residue "A ASP 1123": "OD1" <-> "OD2" Residue "A GLU 1128": "OE1" <-> "OE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 285": "OD1" <-> "OD2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B GLU 574": "OE1" <-> "OE2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 732": "OE1" <-> "OE2" Residue "B ASP 759": "OD1" <-> "OD2" Residue "B TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 851": "OD1" <-> "OD2" Residue "B GLU 972": "OE1" <-> "OE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1056": "OE1" <-> "OE2" Residue "B PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1095": "OE1" <-> "OE2" Residue "B ASP 1111": "OD1" <-> "OD2" Residue "B TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1123": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 285": "OD1" <-> "OD2" Residue "C PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 565": "OD1" <-> "OD2" Residue "C GLU 574": "OE1" <-> "OE2" Residue "C ASP 577": "OD1" <-> "OD2" Residue "C PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 759": "OD1" <-> "OD2" Residue "C PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 851": "OD1" <-> "OD2" Residue "C GLU 972": "OE1" <-> "OE2" Residue "C PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1051": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1093": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1111": "OD1" <-> "OD2" Residue "C TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1123": "OD1" <-> "OD2" Residue "C GLU 1128": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24972 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8326 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 53, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 95 Chain: "B" Number of atoms: 8326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8326 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 53, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 95 Chain: "C" Number of atoms: 8320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8320 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 53, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 101 Time building chain proxies: 12.87, per 1000 atoms: 0.52 Number of scatterers: 24972 At special positions: 0 Unit cell: (148.72, 149.76, 175.76, 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 117 16.00 O 4740 8.00 N 4149 7.00 C 15966 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.04 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 516 " distance=2.04 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 479 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 581 " distance=2.03 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 640 " distance=2.03 Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 722 " - pdb=" SG CYS A 744 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 733 " distance=2.03 Simple disulfide: pdb=" SG CYS A1016 " - pdb=" SG CYS A1027 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.04 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 516 " distance=2.04 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 581 " distance=2.03 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 640 " distance=2.03 Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS B 722 " - pdb=" SG CYS B 744 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 733 " distance=2.03 Simple disulfide: pdb=" SG CYS B1016 " - pdb=" SG CYS B1027 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1110 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.04 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 516 " distance=2.04 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 479 " distance=2.03 Simple disulfide: pdb=" SG CYS C 529 " - pdb=" SG CYS C 581 " distance=2.03 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 640 " distance=2.03 Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.03 Simple disulfide: pdb=" SG CYS C 722 " - pdb=" SG CYS C 744 " distance=2.02 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 733 " distance=2.03 Simple disulfide: pdb=" SG CYS C1016 " - pdb=" SG CYS C1027 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1110 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.11 Conformation dependent library (CDL) restraints added in 4.7 seconds 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 55 sheets defined 24.1% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 374 through 381 removed outlier: 4.113A pdb=" N ASN A 379 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 381 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 607 through 611 removed outlier: 3.542A pdb=" N GLU A 610 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 611 " --> pdb=" O CYS A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 611' Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.565A pdb=" N LEU A 736 " --> pdb=" O GLU A 732 " (cutoff:3.500A) 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 743 through 767 Processing helix chain 'A' and resid 800 through 809 removed outlier: 3.737A pdb=" N LYS A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 840 Processing helix chain 'A' and resid 850 through 868 removed outlier: 3.841A pdb=" N GLN A 856 " --> pdb=" O GLU A 852 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 867 " --> pdb=" O ALA A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 875 removed outlier: 4.046A pdb=" N ALA A 874 " --> pdb=" O TRP A 870 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 875 " --> pdb=" O THR A 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 870 through 875' Processing helix chain 'A' and resid 881 through 892 removed outlier: 3.567A pdb=" N ALA A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 Processing helix chain 'A' and resid 903 through 923 Processing helix chain 'A' and resid 925 through 928 removed outlier: 3.658A pdb=" N ALA A 928 " --> pdb=" O THR A 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 925 through 928' Processing helix chain 'A' and resid 929 through 949 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 removed outlier: 3.606A pdb=" N ILE A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 966 " --> pdb=" O ASN A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 1017 removed outlier: 4.984A pdb=" N VAL A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN A 976 " --> pdb=" O GLU A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'B' and resid 68 through 70 No H-bonds generated for 'chain 'B' and resid 68 through 70' Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 374 through 381 removed outlier: 4.167A pdb=" N ASN B 379 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 607 through 611 removed outlier: 3.573A pdb=" N GLU B 610 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 611 " --> pdb=" O CYS B 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 607 through 611' Processing helix chain 'B' and resid 722 through 727 Processing helix chain 'B' and resid 731 through 738 removed outlier: 3.605A pdb=" N LEU B 736 " --> pdb=" O GLU B 732 " (cutoff:3.500A) 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: 3.513A pdb=" N GLN B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR B 762 " --> pdb=" O GLN B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 809 removed outlier: 3.772A pdb=" N LYS B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 840 Processing helix chain 'B' and resid 850 through 868 removed outlier: 3.905A pdb=" N GLN B 856 " --> pdb=" O GLU B 852 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 859 " --> pdb=" O ALA B 855 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 867 " --> pdb=" O ALA B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 875 removed outlier: 4.182A pdb=" N ALA B 874 " --> pdb=" O TRP B 870 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 875 " --> pdb=" O THR B 871 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 870 through 875' Processing helix chain 'B' and resid 881 through 894 removed outlier: 3.575A pdb=" N ALA B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE B 893 " --> pdb=" O ARG B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 900 Processing helix chain 'B' and resid 903 through 923 Processing helix chain 'B' and resid 925 through 928 removed outlier: 3.654A pdb=" N ALA B 928 " --> pdb=" O THR B 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 925 through 928' Processing helix chain 'B' and resid 929 through 949 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 965 removed outlier: 3.543A pdb=" N ILE B 964 " --> pdb=" O VAL B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 969 through 1017 removed outlier: 4.923A pdb=" N VAL B 975 " --> pdb=" O PRO B 971 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLN B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1124 through 1129 Processing helix chain 'C' and resid 68 through 70 No H-bonds generated for 'chain 'C' and resid 68 through 70' Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 374 through 381 removed outlier: 4.187A pdb=" N ASN C 379 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 381 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 607 through 611 removed outlier: 3.562A pdb=" N GLU C 610 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 611 " --> pdb=" O CYS C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 611' Processing helix chain 'C' and resid 722 through 727 Processing helix chain 'C' and resid 731 through 738 removed outlier: 3.534A pdb=" N LEU C 736 " --> pdb=" O GLU C 732 " (cutoff:3.500A) 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: 3.623A pdb=" N GLN C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 800 through 809 removed outlier: 3.648A pdb=" N LYS C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 840 Processing helix chain 'C' and resid 850 through 868 removed outlier: 3.827A pdb=" N GLN C 856 " --> pdb=" O GLU C 852 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 867 " --> pdb=" O ALA C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 875 removed outlier: 4.089A pdb=" N ALA C 874 " --> pdb=" O TRP C 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 893 removed outlier: 3.612A pdb=" N ALA C 887 " --> pdb=" O ALA C 883 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE C 893 " --> pdb=" O ARG C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 903 through 923 Processing helix chain 'C' and resid 925 through 928 removed outlier: 3.660A pdb=" N ALA C 928 " --> pdb=" O THR C 925 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 925 through 928' Processing helix chain 'C' and resid 929 through 949 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 965 removed outlier: 3.597A pdb=" N ILE C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 1017 removed outlier: 4.947A pdb=" N VAL C 975 " --> pdb=" O PRO C 971 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 1124 through 1129 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.882A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N ASN A 61 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TYR A 260 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 258 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 255 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 259 " --> pdb=" O TYR A 82 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 87 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 178 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 201 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 188 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 192 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ASP A 219 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE A 194 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N HIS A 198 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA A 213 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 36 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.699A pdb=" N GLY C 557 " --> pdb=" O ASP C 565 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.841A pdb=" N ASP A 278 " --> pdb=" O LYS A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 107 through 110 removed outlier: 3.764A pdb=" N SER A 107 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 121 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 159 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 302 through 307 removed outlier: 7.234A pdb=" N VAL A 586 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 585 " --> pdb=" O GLN A 604 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 316 removed outlier: 7.561A pdb=" N GLU A 315 " --> pdb=" O ASN A 531 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASN A 533 " --> pdb=" O GLU A 315 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 539 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.576A pdb=" N LYS A 347 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 388 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL A 386 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 422 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 353 removed outlier: 3.600A pdb=" N CYS A 516 " --> pdb=" O CYS A 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 443 through 445 Processing sheet with id=AB2, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AB3, first strand: chain 'A' and resid 564 through 566 removed outlier: 6.817A pdb=" N GLY A 557 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE A 556 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 644 through 645 removed outlier: 4.628A pdb=" N SER A 675 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 666 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.646A pdb=" N ILE A 661 " --> pdb=" O ILE A 657 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 685 through 686 removed outlier: 6.690A pdb=" N ALA A 685 " --> pdb=" O ILE B 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 695 through 697 removed outlier: 3.754A pdb=" N THR A1060 " --> pdb=" O SER A1081 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN A1090 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLU A1095 " --> pdb=" O GLN A1090 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 701 through 712 removed outlier: 6.920A pdb=" N VAL A1049 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 701 through 712 Processing sheet with id=AC1, first strand: chain 'A' and resid 717 through 720 removed outlier: 4.294A pdb=" N LYS A 717 " --> pdb=" O LEU A 845 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AC3, first strand: chain 'A' and resid 1104 through 1106 Processing sheet with id=AC4, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.189A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN B 61 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR B 260 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 258 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 255 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 84 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY B 259 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 87 " --> pdb=" O ASN B 179 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS B 178 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE B 201 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 180 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 199 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 192 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP B 219 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE B 194 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS B 198 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N ALA B 213 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL B 36 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.264A pdb=" N ASP B 53 " --> pdb=" O ARG B 264 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B 278 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 107 through 110 removed outlier: 3.738A pdb=" N SER B 107 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL B 121 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE B 159 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 302 through 309 removed outlier: 3.557A pdb=" N TYR B 304 " --> pdb=" O VAL B 588 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL B 586 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN B 308 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY B 584 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY B 585 " --> pdb=" O GLN B 604 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 316 removed outlier: 7.616A pdb=" N GLU B 315 " --> pdb=" O ASN B 531 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N ASN B 533 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.842A pdb=" N ASN B 345 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 390 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 347 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL B 386 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 422 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR B 371 " --> pdb=" O GLY B 422 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 352 through 353 removed outlier: 3.612A pdb=" N CYS B 516 " --> pdb=" O CYS B 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 443 through 445 Processing sheet with id=AD3, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AD4, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.782A pdb=" N GLY B 557 " --> pdb=" O ASP B 565 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE B 556 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 644 through 645 removed outlier: 4.597A pdb=" N SER B 675 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN B 666 " --> pdb=" O SER B 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 656 through 658 removed outlier: 6.576A pdb=" N ILE B 661 " --> pdb=" O ILE B 657 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 685 through 686 removed outlier: 6.827A pdb=" N ALA B 685 " --> pdb=" O ILE C 772 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 695 through 697 removed outlier: 3.733A pdb=" N THR B1060 " --> pdb=" O SER B1081 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 701 through 712 removed outlier: 7.184A pdb=" N GLY B1043 " --> pdb=" O SER B1039 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER B1039 " --> pdb=" O GLY B1043 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B1045 " --> pdb=" O PRO B1037 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU B1047 " --> pdb=" O SER B1035 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER B1035 " --> pdb=" O LEU B1047 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL B1049 " --> pdb=" O LEU B1033 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 717 through 720 removed outlier: 4.253A pdb=" N LYS B 717 " --> pdb=" O LEU B 845 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.178A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ASN C 61 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR C 260 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ALA C 255 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR C 86 " --> pdb=" O ALA C 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 84 " --> pdb=" O TYR C 257 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 259 " --> pdb=" O TYR C 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 87 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 178 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE C 201 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE C 192 " --> pdb=" O ASP C 219 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASP C 219 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE C 194 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS C 198 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 8.993A pdb=" N ALA C 213 " --> pdb=" O HIS C 198 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL C 36 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.692A pdb=" N ASP C 278 " --> pdb=" O LYS C 269 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE6, first strand: chain 'C' and resid 107 through 110 removed outlier: 3.792A pdb=" N SER C 107 " --> pdb=" O CYS C 122 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 119 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU C 160 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL C 121 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN C 156 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN C 125 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA C 154 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 302 through 307 removed outlier: 7.246A pdb=" N VAL C 586 " --> pdb=" O THR C 306 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY C 585 " --> pdb=" O GLN C 604 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 316 removed outlier: 7.517A pdb=" N GLU C 315 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ASN C 533 " --> pdb=" O GLU C 315 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 539 " --> pdb=" O PHE C 532 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 347 through 349 removed outlier: 3.684A pdb=" N LYS C 347 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 386 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 422 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR C 371 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL C 424 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 369 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 367 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 352 through 353 removed outlier: 3.629A pdb=" N CYS C 516 " --> pdb=" O CYS C 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 443 through 445 Processing sheet with id=AF3, first strand: chain 'C' and resid 544 through 545 Processing sheet with id=AF4, first strand: chain 'C' and resid 644 through 645 removed outlier: 4.622A pdb=" N SER C 675 " --> pdb=" O GLN C 666 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 666 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 656 through 658 removed outlier: 6.626A pdb=" N ILE C 661 " --> pdb=" O ILE C 657 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 695 through 697 removed outlier: 3.768A pdb=" N THR C1060 " --> pdb=" O SER C1081 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C1062 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE C1079 " --> pdb=" O ALA C1062 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN C1097 " --> pdb=" O VAL C1088 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 701 through 712 removed outlier: 6.903A pdb=" N VAL C1049 " --> pdb=" O LEU C1033 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 701 through 712 Processing sheet with id=AF9, first strand: chain 'C' and resid 717 through 720 removed outlier: 4.325A pdb=" N LYS C 717 " --> pdb=" O LEU C 845 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1104 through 1106 856 hydrogen bonds defined for protein. 2358 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: 10.53 Time building geometry restraints manager: 10.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8049 1.35 - 1.47: 6475 1.47 - 1.60: 10888 1.60 - 1.72: 0 1.72 - 1.84: 147 Bond restraints: 25559 Sorted by residual: bond pdb=" CG LEU C 900 " pdb=" CD1 LEU C 900 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CB CYS C 722 " pdb=" SG CYS C 722 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.78e+00 bond pdb=" CB PRO B 580 " pdb=" CG PRO B 580 " ideal model delta sigma weight residual 1.492 1.550 -0.058 5.00e-02 4.00e+02 1.34e+00 bond pdb=" CB CYS C 157 " pdb=" SG CYS C 157 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" C LEU B 509 " pdb=" N HIS B 510 " ideal model delta sigma weight residual 1.332 1.317 0.015 1.40e-02 5.10e+03 1.17e+00 ... (remaining 25554 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.46: 699 106.46 - 114.07: 14539 114.07 - 121.69: 13440 121.69 - 129.31: 6059 129.31 - 136.93: 96 Bond angle restraints: 34833 Sorted by residual: angle pdb=" C TYR C 480 " pdb=" N PHE C 481 " pdb=" CA PHE C 481 " ideal model delta sigma weight residual 122.31 136.93 -14.62 2.34e+00 1.83e-01 3.90e+01 angle pdb=" C TYR B 480 " pdb=" N PHE B 481 " pdb=" CA PHE B 481 " ideal model delta sigma weight residual 122.31 133.98 -11.67 2.34e+00 1.83e-01 2.49e+01 angle pdb=" N GLY B1108 " pdb=" CA GLY B1108 " pdb=" C GLY B1108 " ideal model delta sigma weight residual 110.20 116.40 -6.20 1.32e+00 5.74e-01 2.20e+01 angle pdb=" N CYS A 423 " pdb=" CA CYS A 423 " pdb=" C CYS A 423 " ideal model delta sigma weight residual 108.24 113.27 -5.03 1.32e+00 5.74e-01 1.45e+01 angle pdb=" N CYS C 423 " pdb=" CA CYS C 423 " pdb=" C CYS C 423 " ideal model delta sigma weight residual 108.45 112.96 -4.51 1.26e+00 6.30e-01 1.28e+01 ... (remaining 34828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13757 17.99 - 35.99: 1154 35.99 - 53.98: 224 53.98 - 71.98: 49 71.98 - 89.97: 30 Dihedral angle restraints: 15214 sinusoidal: 5785 harmonic: 9429 Sorted by residual: dihedral pdb=" CB CYS B 529 " pdb=" SG CYS B 529 " pdb=" SG CYS B 581 " pdb=" CB CYS B 581 " ideal model delta sinusoidal sigma weight residual -86.00 -165.35 79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS A 529 " pdb=" SG CYS A 529 " pdb=" SG CYS A 581 " pdb=" CB CYS A 581 " ideal model delta sinusoidal sigma weight residual -86.00 -164.56 78.56 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CB CYS C 529 " pdb=" SG CYS C 529 " pdb=" SG CYS C 581 " pdb=" CB CYS C 581 " ideal model delta sinusoidal sigma weight residual -86.00 -164.21 78.21 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 15211 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2779 0.042 - 0.085: 863 0.085 - 0.127: 319 0.127 - 0.170: 21 0.170 - 0.212: 5 Chirality restraints: 3987 Sorted by residual: chirality pdb=" CB THR C 86 " pdb=" CA THR C 86 " pdb=" OG1 THR C 86 " pdb=" CG2 THR C 86 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB THR B 86 " pdb=" CA THR B 86 " pdb=" OG1 THR B 86 " pdb=" CG2 THR B 86 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CB VAL A1078 " pdb=" CA VAL A1078 " pdb=" CG1 VAL A1078 " pdb=" CG2 VAL A1078 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.76e-01 ... (remaining 3984 not shown) Planarity restraints: 4511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 327 " 0.090 5.00e-02 4.00e+02 1.37e-01 3.00e+01 pdb=" N PRO C 328 " -0.237 5.00e-02 4.00e+02 pdb=" CA PRO C 328 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 328 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 511 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO B 512 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 512 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 512 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 511 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO C 512 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 512 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 512 " -0.039 5.00e-02 4.00e+02 ... (remaining 4508 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 590 2.68 - 3.23: 24574 3.23 - 3.79: 37411 3.79 - 4.34: 52876 4.34 - 4.90: 88107 Nonbonded interactions: 203558 Sorted by model distance: nonbonded pdb=" OE1 GLU C 803 " pdb=" OG SER C1039 " model vdw 2.124 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 265 " model vdw 2.128 2.440 nonbonded pdb=" OE1 GLU A 803 " pdb=" OG SER A1039 " model vdw 2.143 2.440 nonbonded pdb=" OE1 GLN C 52 " pdb=" OG1 THR C 265 " model vdw 2.146 2.440 nonbonded pdb=" OE1 GLN A 52 " pdb=" OG1 THR A 265 " model vdw 2.157 2.440 ... (remaining 203553 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 147 or (resid 148 through 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 1131)) selection = (chain 'B' and (resid 14 through 147 or (resid 148 through 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 1131)) 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 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: 0.000 Extract box with map and model: 7.280 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 66.850 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.100 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.004 0.058 25559 Z= 0.243 Angle : 0.661 14.622 34833 Z= 0.379 Chirality : 0.046 0.212 3987 Planarity : 0.005 0.137 4511 Dihedral : 14.391 89.974 9028 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.14), residues: 3219 helix: -0.01 (0.20), residues: 669 sheet: -1.99 (0.22), residues: 603 loop : -2.81 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 870 HIS 0.011 0.001 HIS B 236 PHE 0.041 0.002 PHE B 890 TYR 0.017 0.001 TYR C 342 ARG 0.008 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.663 Fit side-chains REVERT: C 886 MET cc_start: 0.7789 (tpp) cc_final: 0.7557 (mmt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3258 time to fit residues: 125.0682 Evaluate side-chains 176 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.8980 chunk 243 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 251 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 0.0050 chunk 187 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1097 GLN B 140 ASN B 597 ASN B 885 GLN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 ASN C 885 GLN C1109 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25559 Z= 0.209 Angle : 0.564 8.681 34833 Z= 0.295 Chirality : 0.045 0.152 3987 Planarity : 0.004 0.090 4511 Dihedral : 4.886 21.404 3456 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.98 % Allowed : 5.77 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.14), residues: 3219 helix: 0.64 (0.21), residues: 639 sheet: -1.60 (0.21), residues: 624 loop : -2.51 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 95 HIS 0.008 0.001 HIS C 236 PHE 0.048 0.001 PHE C 329 TYR 0.022 0.001 TYR A1051 ARG 0.004 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 2.471 Fit side-chains REVERT: A 83 PHE cc_start: 0.7230 (t80) cc_final: 0.6322 (t80) REVERT: B 568 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7176 (ptm160) outliers start: 27 outliers final: 23 residues processed: 222 average time/residue: 0.3026 time to fit residues: 115.3859 Evaluate side-chains 196 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1097 GLN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 198 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 315 optimal weight: 0.6980 chunk 260 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25559 Z= 0.284 Angle : 0.565 9.097 34833 Z= 0.293 Chirality : 0.045 0.149 3987 Planarity : 0.004 0.081 4511 Dihedral : 4.847 20.509 3456 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.34 % Allowed : 8.89 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 3219 helix: 0.55 (0.21), residues: 657 sheet: -1.58 (0.20), residues: 660 loop : -2.42 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 64 HIS 0.007 0.001 HIS B 236 PHE 0.019 0.001 PHE B 890 TYR 0.021 0.001 TYR A1051 ARG 0.002 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 2.781 Fit side-chains REVERT: B 568 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7069 (ptm160) outliers start: 37 outliers final: 27 residues processed: 208 average time/residue: 0.3104 time to fit residues: 109.8688 Evaluate side-chains 203 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.5980 chunk 219 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25559 Z= 0.306 Angle : 0.559 9.076 34833 Z= 0.291 Chirality : 0.045 0.157 3987 Planarity : 0.004 0.069 4511 Dihedral : 4.808 19.827 3456 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 1.89 % Allowed : 10.20 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.15), residues: 3219 helix: 0.60 (0.21), residues: 657 sheet: -1.50 (0.20), residues: 666 loop : -2.38 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 64 HIS 0.007 0.001 HIS A 236 PHE 0.020 0.001 PHE B 890 TYR 0.022 0.001 TYR B 256 ARG 0.005 0.000 ARG C 348 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 191 time to evaluate : 2.491 Fit side-chains REVERT: B 568 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6984 (ptm160) outliers start: 52 outliers final: 38 residues processed: 231 average time/residue: 0.3008 time to fit residues: 119.8526 Evaluate side-chains 214 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 175 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Chi-restraints excluded: chain C residue 769 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.4980 chunk 176 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 214 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 158 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.123 25559 Z= 0.557 Angle : 0.687 11.098 34833 Z= 0.352 Chirality : 0.050 0.229 3987 Planarity : 0.004 0.063 4511 Dihedral : 5.220 20.668 3456 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 2.54 % Allowed : 11.54 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.14), residues: 3219 helix: 0.17 (0.20), residues: 675 sheet: -1.76 (0.20), residues: 687 loop : -2.50 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 64 HIS 0.008 0.001 HIS C 236 PHE 0.039 0.002 PHE B 890 TYR 0.031 0.002 TYR B 256 ARG 0.005 0.000 ARG B 889 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 193 time to evaluate : 2.734 Fit side-chains REVERT: B 568 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6830 (ptm160) outliers start: 70 outliers final: 53 residues processed: 248 average time/residue: 0.3056 time to fit residues: 128.5658 Evaluate side-chains 235 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 181 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1089 THR Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 1065 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.5980 chunk 279 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 310 optimal weight: 0.7980 chunk 257 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 163 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 763 GLN ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25559 Z= 0.173 Angle : 0.534 10.240 34833 Z= 0.278 Chirality : 0.044 0.169 3987 Planarity : 0.004 0.061 4511 Dihedral : 4.711 19.242 3456 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.10 % Allowed : 12.45 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.15), residues: 3219 helix: 0.95 (0.21), residues: 639 sheet: -1.51 (0.20), residues: 696 loop : -2.25 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.011 0.001 HIS A 198 PHE 0.018 0.001 PHE A 166 TYR 0.019 0.001 TYR C1051 ARG 0.005 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 2.607 Fit side-chains REVERT: A 233 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5504 (tt) REVERT: C 934 ASP cc_start: 0.7480 (m-30) cc_final: 0.7279 (m-30) outliers start: 58 outliers final: 40 residues processed: 234 average time/residue: 0.3220 time to fit residues: 129.4390 Evaluate side-chains 222 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 371 TYR Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 GLU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Chi-restraints excluded: chain C residue 1089 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 176 optimal weight: 0.9980 chunk 226 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 173 optimal weight: 0.1980 chunk 309 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 188 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 25559 Z= 0.399 Angle : 0.605 10.952 34833 Z= 0.311 Chirality : 0.047 0.286 3987 Planarity : 0.004 0.061 4511 Dihedral : 4.874 19.983 3456 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.43 % Allowed : 12.70 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.15), residues: 3219 helix: 0.55 (0.21), residues: 657 sheet: -1.55 (0.20), residues: 696 loop : -2.39 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 64 HIS 0.009 0.001 HIS A 198 PHE 0.024 0.002 PHE B1105 TYR 0.025 0.002 TYR B 256 ARG 0.004 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 187 time to evaluate : 2.700 Fit side-chains REVERT: A 233 LEU cc_start: 0.5934 (OUTLIER) cc_final: 0.5564 (tt) REVERT: C 934 ASP cc_start: 0.7458 (m-30) cc_final: 0.7252 (m-30) outliers start: 67 outliers final: 55 residues processed: 242 average time/residue: 0.3012 time to fit residues: 125.9141 Evaluate side-chains 235 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 179 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1128 GLU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 423 CYS Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 722 CYS Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1089 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 184 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 196 optimal weight: 0.5980 chunk 210 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 758 GLN ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25559 Z= 0.163 Angle : 0.518 10.676 34833 Z= 0.269 Chirality : 0.043 0.252 3987 Planarity : 0.004 0.055 4511 Dihedral : 4.514 19.412 3456 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.89 % Allowed : 13.24 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 3219 helix: 0.98 (0.21), residues: 657 sheet: -1.39 (0.20), residues: 693 loop : -2.19 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.007 0.001 HIS B 236 PHE 0.021 0.001 PHE B 83 TYR 0.020 0.001 TYR C1051 ARG 0.005 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 189 time to evaluate : 2.744 Fit side-chains REVERT: A 233 LEU cc_start: 0.5783 (OUTLIER) cc_final: 0.5477 (tt) REVERT: B 278 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6534 (m-30) REVERT: B 344 TRP cc_start: 0.6681 (p-90) cc_final: 0.6425 (p-90) outliers start: 52 outliers final: 42 residues processed: 229 average time/residue: 0.3501 time to fit residues: 137.7716 Evaluate side-chains 223 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 179 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1084 THR Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1089 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.8980 chunk 296 optimal weight: 0.9980 chunk 270 optimal weight: 8.9990 chunk 288 optimal weight: 0.7980 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 226 optimal weight: 0.0870 chunk 88 optimal weight: 0.1980 chunk 260 optimal weight: 9.9990 chunk 272 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** B1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25559 Z= 0.164 Angle : 0.512 11.069 34833 Z= 0.263 Chirality : 0.043 0.241 3987 Planarity : 0.004 0.070 4511 Dihedral : 4.355 18.876 3456 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.74 % Allowed : 13.24 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.15), residues: 3219 helix: 1.15 (0.21), residues: 657 sheet: -1.13 (0.21), residues: 660 loop : -2.12 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 95 HIS 0.007 0.001 HIS A 236 PHE 0.021 0.001 PHE A 166 TYR 0.019 0.001 TYR C1051 ARG 0.005 0.000 ARG A 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 199 time to evaluate : 2.776 Fit side-chains REVERT: A 233 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5368 (tt) REVERT: B 278 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6545 (m-30) REVERT: B 344 TRP cc_start: 0.6644 (p-90) cc_final: 0.6431 (p-90) outliers start: 48 outliers final: 40 residues processed: 236 average time/residue: 0.3059 time to fit residues: 122.9676 Evaluate side-chains 231 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 189 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1089 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.3980 chunk 304 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 211 optimal weight: 0.0030 chunk 319 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 254 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN B 140 ASN ** B 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25559 Z= 0.254 Angle : 0.539 11.150 34833 Z= 0.277 Chirality : 0.044 0.232 3987 Planarity : 0.004 0.066 4511 Dihedral : 4.458 19.408 3456 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.74 % Allowed : 13.50 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 3219 helix: 1.00 (0.21), residues: 657 sheet: -1.12 (0.21), residues: 663 loop : -2.13 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.007 0.001 HIS A 236 PHE 0.021 0.001 PHE A 166 TYR 0.020 0.001 TYR C1051 ARG 0.005 0.000 ARG B 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 188 time to evaluate : 3.141 Fit side-chains REVERT: A 233 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5516 (tt) REVERT: B 278 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6659 (m-30) REVERT: B 344 TRP cc_start: 0.6750 (p-90) cc_final: 0.6528 (p-90) outliers start: 48 outliers final: 43 residues processed: 226 average time/residue: 0.3072 time to fit residues: 118.4291 Evaluate side-chains 225 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 180 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 1065 ILE Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 325 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 843 THR Chi-restraints excluded: chain B residue 1065 ILE Chi-restraints excluded: chain B residue 1088 VAL Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 325 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 424 VAL Chi-restraints excluded: chain C residue 516 CYS Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 1065 ILE Chi-restraints excluded: chain C residue 1089 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 46 optimal weight: 0.0370 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN ** B 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.193916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142662 restraints weight = 30037.683| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.13 r_work: 0.3203 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25559 Z= 0.262 Angle : 0.545 11.070 34833 Z= 0.280 Chirality : 0.045 0.228 3987 Planarity : 0.004 0.065 4511 Dihedral : 4.497 19.397 3456 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.74 % Allowed : 13.50 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.15), residues: 3219 helix: 0.95 (0.21), residues: 657 sheet: -1.31 (0.20), residues: 699 loop : -2.15 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 64 HIS 0.007 0.001 HIS B 236 PHE 0.021 0.001 PHE A 166 TYR 0.019 0.001 TYR B 256 ARG 0.006 0.000 ARG B 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4625.21 seconds wall clock time: 85 minutes 4.37 seconds (5104.37 seconds total)