Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 07:36:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/04_2023/7vhm_31999.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/04_2023/7vhm_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_31999/04_2023/7vhm_31999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/04_2023/7vhm_31999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/04_2023/7vhm_31999.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhm_31999/04_2023/7vhm_31999.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 12.81, per 1000 atoms: 0.51 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: 9.57 Conformation dependent library (CDL) restraints added in 3.7 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: 2.09 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: 11.00 Time building geometry restraints manager: 10.28 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.170 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 64.300 Find NCS groups from input model: 1.490 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.580 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.781 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3257 time to fit residues: 124.8303 Evaluate side-chains 176 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 3.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8973 ------------------------------------------------------------------------------- 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: 0.0826 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= 0.207 Angle : 0.562 8.734 34833 Z= 0.295 Chirality : 0.045 0.149 3987 Planarity : 0.004 0.090 4511 Dihedral : 4.884 21.419 3456 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 0.98 % 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: 0.65 (0.21), residues: 639 sheet: -1.59 (0.21), residues: 624 loop : -2.50 (0.13), residues: 1956 *********************** 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 : 3.064 Fit side-chains outliers start: 27 outliers final: 22 residues processed: 222 average time/residue: 0.3208 time to fit residues: 122.3131 Evaluate side-chains 194 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 3.042 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2256 time to fit residues: 13.8545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 292 optimal weight: 9.9990 chunk 315 optimal weight: 0.7980 chunk 260 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 758 GLN C 30 ASN ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 25559 Z= 0.210 Angle : 0.539 9.515 34833 Z= 0.280 Chirality : 0.044 0.141 3987 Planarity : 0.004 0.081 4511 Dihedral : 4.710 20.557 3456 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer Outliers : 0.65 % 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: -2.16 (0.15), residues: 3219 helix: 0.87 (0.21), residues: 639 sheet: -1.56 (0.21), residues: 624 loop : -2.31 (0.13), residues: 1956 *********************** 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 206 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 188 time to evaluate : 2.833 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 204 average time/residue: 0.3395 time to fit residues: 117.7290 Evaluate side-chains 185 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 2.699 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2234 time to fit residues: 6.8367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.0020 chunk 219 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 139 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 310 optimal weight: 0.2980 chunk 153 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1241 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= 0.182 Angle : 0.515 10.504 34833 Z= 0.267 Chirality : 0.043 0.154 3987 Planarity : 0.004 0.067 4511 Dihedral : 4.535 20.117 3456 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer Outliers : 1.02 % 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: -2.02 (0.15), residues: 3219 helix: 0.92 (0.21), residues: 657 sheet: -1.40 (0.21), residues: 624 loop : -2.25 (0.13), residues: 1938 *********************** 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 232 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 2.793 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 223 average time/residue: 0.3237 time to fit residues: 122.4217 Evaluate side-chains 201 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 2.907 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2242 time to fit residues: 11.2583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 0.0030 chunk 176 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 214 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 158 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 overall best weight: 3.5196 ------------------------------------------------------------------------------- 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: 0.7820 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.112 25559 Z= 0.518 Angle : 0.664 10.901 34833 Z= 0.339 Chirality : 0.049 0.236 3987 Planarity : 0.004 0.064 4511 Dihedral : 5.026 20.362 3456 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 1.09 % 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: -2.37 (0.14), residues: 3219 helix: 0.35 (0.21), residues: 657 sheet: -1.56 (0.20), residues: 702 loop : -2.40 (0.14), residues: 1860 *********************** 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 217 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 3.007 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 216 average time/residue: 0.3233 time to fit residues: 119.2983 Evaluate side-chains 194 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 2.630 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2145 time to fit residues: 10.2497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.0970 chunk 279 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 257 optimal weight: 9.9990 chunk 143 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 163 optimal weight: 10.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1404 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= 0.178 Angle : 0.527 10.292 34833 Z= 0.273 Chirality : 0.044 0.251 3987 Planarity : 0.004 0.056 4511 Dihedral : 4.595 19.372 3456 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 1.05 % 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: -1.93 (0.15), residues: 3219 helix: 1.02 (0.21), residues: 639 sheet: -1.29 (0.21), residues: 654 loop : -2.20 (0.13), residues: 1926 *********************** 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 221 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 2.770 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 212 average time/residue: 0.3221 time to fit residues: 115.2379 Evaluate side-chains 194 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 2.827 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2252 time to fit residues: 9.8752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 173 optimal weight: 0.6980 chunk 309 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 25559 Z= 0.333 Angle : 0.575 10.912 34833 Z= 0.295 Chirality : 0.046 0.241 3987 Planarity : 0.004 0.054 4511 Dihedral : 4.700 19.558 3456 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.15), residues: 3219 helix: 0.75 (0.21), residues: 657 sheet: -1.47 (0.20), residues: 696 loop : -2.29 (0.14), residues: 1866 *********************** 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 204 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.846 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 200 average time/residue: 0.3335 time to fit residues: 112.8732 Evaluate side-chains 187 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 2.658 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2177 time to fit residues: 7.4853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 210 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 243 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN C 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1561 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 : 0.517 10.560 34833 Z= 0.266 Chirality : 0.044 0.230 3987 Planarity : 0.004 0.052 4511 Dihedral : 4.459 23.258 3456 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.87 % 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: -1.88 (0.15), residues: 3219 helix: 1.04 (0.21), residues: 657 sheet: -1.35 (0.20), residues: 690 loop : -2.16 (0.14), residues: 1872 *********************** 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 215 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 2.705 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 207 average time/residue: 0.3448 time to fit residues: 120.5780 Evaluate side-chains 188 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 2.912 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2562 time to fit residues: 8.4985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 chunk 270 optimal weight: 6.9990 chunk 288 optimal weight: 0.0770 chunk 173 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 260 optimal weight: 20.0000 chunk 272 optimal weight: 0.7980 chunk 287 optimal weight: 0.0980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 25559 Z= 0.159 Angle : 0.512 10.969 34833 Z= 0.263 Chirality : 0.043 0.215 3987 Planarity : 0.004 0.060 4511 Dihedral : 4.324 19.350 3456 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer Outliers : 0.07 % 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: -1.66 (0.15), residues: 3219 helix: 1.18 (0.21), residues: 663 sheet: -1.05 (0.21), residues: 657 loop : -2.07 (0.14), residues: 1899 *********************** 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 191 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 3.126 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 190 average time/residue: 0.3291 time to fit residues: 107.3876 Evaluate side-chains 184 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 182 time to evaluate : 2.927 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2159 time to fit residues: 4.9895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 chunk 144 optimal weight: 10.0000 chunk 211 optimal weight: 0.0770 chunk 319 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 156 optimal weight: 0.0170 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 C 597 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 25559 Z= 0.152 Angle : 0.501 10.909 34833 Z= 0.257 Chirality : 0.043 0.210 3987 Planarity : 0.004 0.066 4511 Dihedral : 4.182 19.210 3456 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.15), residues: 3219 helix: 1.37 (0.21), residues: 663 sheet: -1.07 (0.21), residues: 648 loop : -1.95 (0.14), residues: 1908 ********************** 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 199 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 195 time to evaluate : 3.037 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 198 average time/residue: 0.3433 time to fit residues: 115.1654 Evaluate side-chains 177 residues out of total 2823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 2.847 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2250 time to fit residues: 4.4358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 234 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 ASN A 385 ASN A 941 GLN C 385 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.192832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.142690 restraints weight = 30087.764| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.87 r_work: 0.3225 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.081 25559 Z= 0.373 Angle : 0.590 12.407 34833 Z= 0.300 Chirality : 0.046 0.207 3987 Planarity : 0.004 0.064 4511 Dihedral : 4.537 19.607 3456 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer Outliers : 0.29 % 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: -1.83 (0.15), residues: 3219 helix: 0.92 (0.21), residues: 657 sheet: -1.21 (0.20), residues: 708 loop : -2.11 (0.14), residues: 1854 =============================================================================== Job complete usr+sys time: 4427.88 seconds wall clock time: 82 minutes 23.14 seconds (4943.14 seconds total)