Starting phenix.real_space_refine on Tue Mar 19 17:19:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/03_2024/3jcl_6526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/03_2024/3jcl_6526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/03_2024/3jcl_6526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/03_2024/3jcl_6526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/03_2024/3jcl_6526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/03_2024/3jcl_6526.pdb" } resolution = 4.0 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= 0.006 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 144 5.16 5 C 15702 2.51 5 N 4218 2.21 5 O 4758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 376": "OD1" <-> "OD2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 376": "OD1" <-> "OD2" Residue "C TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 887": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 24822 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8274 Classifications: {'peptide': 1067} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1022} Chain breaks: 1 Chain: "B" Number of atoms: 8274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8274 Classifications: {'peptide': 1067} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1022} Chain breaks: 1 Chain: "C" Number of atoms: 8274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8274 Classifications: {'peptide': 1067} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1022} Chain breaks: 1 Time building chain proxies: 11.79, per 1000 atoms: 0.47 Number of scatterers: 24822 At special positions: 0 Unit cell: (140.16, 137.24, 148.92, 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 144 16.00 O 4758 8.00 N 4218 7.00 C 15702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 158 " distance=2.02 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 187 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 246 " distance=2.13 Simple disulfide: pdb=" SG CYS A 284 " - pdb=" SG CYS A 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 354 " distance=2.02 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 425 " distance=2.72 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 564 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 479 " distance=2.02 Simple disulfide: pdb=" SG CYS A 481 " - pdb=" SG CYS A 528 " distance=2.03 Simple disulfide: pdb=" SG CYS A 490 " - pdb=" SG CYS A 517 " distance=2.02 Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 526 " distance=2.07 Simple disulfide: pdb=" SG CYS A 541 " - pdb=" SG CYS A 547 " distance=2.04 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 633 " distance=2.07 Simple disulfide: pdb=" SG CYS A 658 " - pdb=" SG CYS A 682 " distance=2.04 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 706 " distance=2.03 Simple disulfide: pdb=" SG CYS A 775 " - pdb=" SG CYS A 797 " distance=2.11 Simple disulfide: pdb=" SG CYS A 780 " - pdb=" SG CYS A 786 " distance=2.04 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 905 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1093 " distance=2.05 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 158 " distance=2.02 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 187 " distance=2.04 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 246 " distance=2.13 Simple disulfide: pdb=" SG CYS B 284 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 354 " distance=2.02 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 425 " distance=2.72 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 479 " distance=2.02 Simple disulfide: pdb=" SG CYS B 481 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 490 " - pdb=" SG CYS B 517 " distance=2.02 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 526 " distance=2.07 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 547 " distance=2.04 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 633 " distance=2.08 Simple disulfide: pdb=" SG CYS B 658 " - pdb=" SG CYS B 682 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 706 " distance=2.03 Simple disulfide: pdb=" SG CYS B 775 " - pdb=" SG CYS B 797 " distance=2.11 Simple disulfide: pdb=" SG CYS B 780 " - pdb=" SG CYS B 786 " distance=2.04 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 905 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1093 " distance=2.05 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 158 " distance=2.02 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 165 " - pdb=" SG CYS C 246 " distance=2.13 Simple disulfide: pdb=" SG CYS C 284 " - pdb=" SG CYS C 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 354 " distance=2.02 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 425 " distance=2.72 Simple disulfide: pdb=" SG CYS C 384 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 479 " distance=2.02 Simple disulfide: pdb=" SG CYS C 481 " - pdb=" SG CYS C 528 " distance=2.03 Simple disulfide: pdb=" SG CYS C 490 " - pdb=" SG CYS C 517 " distance=2.02 Simple disulfide: pdb=" SG CYS C 507 " - pdb=" SG CYS C 526 " distance=2.07 Simple disulfide: pdb=" SG CYS C 541 " - pdb=" SG CYS C 547 " distance=2.04 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 633 " distance=2.08 Simple disulfide: pdb=" SG CYS C 658 " - pdb=" SG CYS C 682 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 706 " distance=2.03 Simple disulfide: pdb=" SG CYS C 775 " - pdb=" SG CYS C 797 " distance=2.11 Simple disulfide: pdb=" SG CYS C 780 " - pdb=" SG CYS C 786 " distance=2.04 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 905 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1093 " distance=2.05 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: 9.39 Conformation dependent library (CDL) restraints added in 4.6 seconds 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5976 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 39 sheets defined 32.7% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP A 334 " --> pdb=" O ASN A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 376 through 381 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 657 through 664 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.724A pdb=" N THR A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET A 749 " --> pdb=" O GLY A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE A 755 " --> pdb=" O PRO A 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 752 through 755' Processing helix chain 'A' and resid 774 through 780 Processing helix chain 'A' and resid 783 through 791 removed outlier: 3.777A pdb=" N GLN A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 824 removed outlier: 3.502A pdb=" N CYS A 797 " --> pdb=" O TYR A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 879 removed outlier: 4.370A pdb=" N PHE A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 894 Processing helix chain 'A' and resid 895 through 897 No H-bonds generated for 'chain 'A' and resid 895 through 897' Processing helix chain 'A' and resid 902 through 910 removed outlier: 4.672A pdb=" N SER A 908 " --> pdb=" O LEU A 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 909 " --> pdb=" O CYS A 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 910 " --> pdb=" O VAL A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 937 Processing helix chain 'A' and resid 938 through 945 Processing helix chain 'A' and resid 947 through 958 Processing helix chain 'A' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1019 No H-bonds generated for 'chain 'A' and resid 1017 through 1019' Processing helix chain 'A' and resid 1026 through 1032 Processing helix chain 'A' and resid 1035 through 1083 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP B 334 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 479 through 483 Processing helix chain 'B' and resid 520 through 524 Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.724A pdb=" N THR B 721 " --> pdb=" O SER B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET B 749 " --> pdb=" O GLY B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE B 755 " --> pdb=" O PRO B 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 752 through 755' Processing helix chain 'B' and resid 774 through 780 Processing helix chain 'B' and resid 783 through 791 removed outlier: 3.776A pdb=" N GLN B 789 " --> pdb=" O ALA B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 824 removed outlier: 3.501A pdb=" N CYS B 797 " --> pdb=" O TYR B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 879 removed outlier: 4.369A pdb=" N PHE B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS B 879 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 894 Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 902 through 910 removed outlier: 4.672A pdb=" N SER B 908 " --> pdb=" O LEU B 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 909 " --> pdb=" O CYS B 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN B 910 " --> pdb=" O VAL B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 937 Processing helix chain 'B' and resid 938 through 945 Processing helix chain 'B' and resid 947 through 958 Processing helix chain 'B' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1026 through 1032 Processing helix chain 'B' and resid 1035 through 1083 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 330 through 336 removed outlier: 3.925A pdb=" N TRP C 334 " --> pdb=" O ASN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 396 through 398 No H-bonds generated for 'chain 'C' and resid 396 through 398' Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 466 through 471 Processing helix chain 'C' and resid 479 through 483 Processing helix chain 'C' and resid 520 through 524 Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'C' and resid 657 through 664 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.725A pdb=" N THR C 721 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 751 removed outlier: 3.842A pdb=" N MET C 749 " --> pdb=" O GLY C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 755 removed outlier: 4.079A pdb=" N PHE C 755 " --> pdb=" O PRO C 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 752 through 755' Processing helix chain 'C' and resid 774 through 780 Processing helix chain 'C' and resid 783 through 791 removed outlier: 3.777A pdb=" N GLN C 789 " --> pdb=" O ALA C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 824 removed outlier: 3.502A pdb=" N CYS C 797 " --> pdb=" O TYR C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 879 removed outlier: 4.369A pdb=" N PHE C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 894 Processing helix chain 'C' and resid 895 through 897 No H-bonds generated for 'chain 'C' and resid 895 through 897' Processing helix chain 'C' and resid 902 through 910 removed outlier: 4.671A pdb=" N SER C 908 " --> pdb=" O LEU C 904 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 909 " --> pdb=" O CYS C 905 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN C 910 " --> pdb=" O VAL C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 937 Processing helix chain 'C' and resid 938 through 945 Processing helix chain 'C' and resid 947 through 958 Processing helix chain 'C' and resid 968 through 988 removed outlier: 3.788A pdb=" N PHE C 988 " --> pdb=" O ILE C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1016 removed outlier: 3.947A pdb=" N LEU C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1019 No H-bonds generated for 'chain 'C' and resid 1017 through 1019' Processing helix chain 'C' and resid 1026 through 1032 Processing helix chain 'C' and resid 1035 through 1083 Processing sheet with id= A, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN A 26 " --> pdb=" O VAL A 87 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE A 76 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LYS A 75 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 103 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 213 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 229 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA A 215 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN A 267 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP A 283 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 269 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA A 281 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN A 271 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 82 through 83 removed outlier: 6.666A pdb=" N THR A 163 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 98 through 99 removed outlier: 3.899A pdb=" N THR A 125 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 154 " --> pdb=" O CYS A 187 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N CYS A 187 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY A 304 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR A 627 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN A 617 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 609 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 347 through 351 removed outlier: 7.138A pdb=" N THR A 430 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA A 367 " --> pdb=" O THR A 430 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 354 through 356 Processing sheet with id= J, first strand: chain 'A' and resid 442 through 455 removed outlier: 5.615A pdb=" N SER A 444 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 543 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 448 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER A 537 " --> pdb=" O TYR A 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 452 " --> pdb=" O GLY A 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY A 535 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP A 454 " --> pdb=" O PHE A 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 533 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 688 through 694 removed outlier: 6.294A pdb=" N LYS A 711 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU A 692 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 699 " --> pdb=" O VAL A 707 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 757 through 764 Processing sheet with id= M, first strand: chain 'A' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS A 770 " --> pdb=" O LEU A 915 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN B 26 " --> pdb=" O VAL B 87 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE B 76 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LYS B 75 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY B 103 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B 213 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER B 229 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 215 " --> pdb=" O LEU B 227 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN B 267 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP B 283 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU B 269 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 281 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B 271 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 82 through 83 removed outlier: 6.665A pdb=" N THR B 163 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 98 through 99 removed outlier: 3.900A pdb=" N THR B 125 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN B 154 " --> pdb=" O CYS B 187 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N CYS B 187 " --> pdb=" O GLN B 154 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY B 304 " --> pdb=" O ALA B 641 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR B 627 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN B 617 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 609 " --> pdb=" O ASN B 617 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 347 through 351 removed outlier: 7.138A pdb=" N THR B 430 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA B 367 " --> pdb=" O THR B 430 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 354 through 356 Processing sheet with id= W, first strand: chain 'B' and resid 442 through 455 removed outlier: 5.614A pdb=" N SER B 444 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 543 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 448 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER B 537 " --> pdb=" O TYR B 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE B 452 " --> pdb=" O GLY B 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY B 535 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP B 454 " --> pdb=" O PHE B 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 533 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 688 through 694 removed outlier: 6.296A pdb=" N LYS B 711 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU B 692 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 757 through 764 Processing sheet with id= Z, first strand: chain 'B' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS B 770 " --> pdb=" O LEU B 915 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.635A pdb=" N ASN C 26 " --> pdb=" O VAL C 87 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'C' and resid 37 through 41 removed outlier: 5.060A pdb=" N PHE C 76 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS C 75 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 103 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C 213 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER C 229 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA C 215 " --> pdb=" O LEU C 227 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 61 through 70 removed outlier: 7.707A pdb=" N GLN C 267 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP C 283 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU C 269 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA C 281 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN C 271 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.666A pdb=" N THR C 163 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 98 through 99 removed outlier: 3.900A pdb=" N THR C 125 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN C 154 " --> pdb=" O CYS C 187 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N CYS C 187 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 304 through 307 removed outlier: 6.284A pdb=" N GLY C 304 " --> pdb=" O ALA C 641 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 318 through 321 removed outlier: 4.188A pdb=" N THR C 627 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASN C 617 " --> pdb=" O ILE C 630 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 609 " --> pdb=" O ASN C 617 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 347 through 351 removed outlier: 7.139A pdb=" N THR C 430 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA C 367 " --> pdb=" O THR C 430 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 354 through 356 Processing sheet with id= AJ, first strand: chain 'C' and resid 442 through 455 removed outlier: 5.614A pdb=" N SER C 444 " --> pdb=" O VAL C 543 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 543 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 448 " --> pdb=" O ASP C 539 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N SER C 537 " --> pdb=" O TYR C 450 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE C 452 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY C 535 " --> pdb=" O PHE C 452 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 454 " --> pdb=" O PHE C 533 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 533 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 688 through 694 removed outlier: 6.295A pdb=" N LYS C 711 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU C 692 " --> pdb=" O LYS C 711 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU C 699 " --> pdb=" O VAL C 707 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 757 through 764 Processing sheet with id= AM, first strand: chain 'C' and resid 770 through 773 removed outlier: 4.032A pdb=" N LYS C 770 " --> pdb=" O LEU C 915 " (cutoff:3.500A) 1104 hydrogen bonds defined for protein. 3051 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: 10.23 Time building geometry restraints manager: 10.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5100 1.32 - 1.46: 8990 1.46 - 1.60: 11104 1.60 - 1.75: 27 1.75 - 1.89: 153 Bond restraints: 25374 Sorted by residual: bond pdb=" CB PHE A 270 " pdb=" CG PHE A 270 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.56e+01 bond pdb=" CB PHE C 270 " pdb=" CG PHE C 270 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.56e+01 bond pdb=" CB PHE B 270 " pdb=" CG PHE B 270 " ideal model delta sigma weight residual 1.502 1.366 0.136 2.30e-02 1.89e+03 3.49e+01 bond pdb=" CB LEU A 300 " pdb=" CG LEU A 300 " ideal model delta sigma weight residual 1.530 1.426 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB LEU B 300 " pdb=" CG LEU B 300 " ideal model delta sigma weight residual 1.530 1.427 0.103 2.00e-02 2.50e+03 2.67e+01 ... (remaining 25369 not shown) Histogram of bond angle deviations from ideal: 93.63 - 101.72: 83 101.72 - 109.81: 5637 109.81 - 117.90: 13427 117.90 - 125.99: 15120 125.99 - 134.08: 302 Bond angle restraints: 34569 Sorted by residual: angle pdb=" N VAL A 946 " pdb=" CA VAL A 946 " pdb=" CB VAL A 946 " ideal model delta sigma weight residual 110.17 98.69 11.48 1.11e+00 8.12e-01 1.07e+02 angle pdb=" C ALA A 944 " pdb=" CA ALA A 944 " pdb=" CB ALA A 944 " ideal model delta sigma weight residual 110.79 93.63 17.16 1.66e+00 3.63e-01 1.07e+02 angle pdb=" N VAL C 946 " pdb=" CA VAL C 946 " pdb=" CB VAL C 946 " ideal model delta sigma weight residual 110.17 98.72 11.45 1.11e+00 8.12e-01 1.06e+02 angle pdb=" N VAL B 946 " pdb=" CA VAL B 946 " pdb=" CB VAL B 946 " ideal model delta sigma weight residual 110.17 98.72 11.45 1.11e+00 8.12e-01 1.06e+02 angle pdb=" C ALA C 944 " pdb=" CA ALA C 944 " pdb=" CB ALA C 944 " ideal model delta sigma weight residual 110.79 93.69 17.10 1.66e+00 3.63e-01 1.06e+02 ... (remaining 34564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 14645 18.10 - 36.20: 373 36.20 - 54.30: 79 54.30 - 72.40: 59 72.40 - 90.50: 12 Dihedral angle restraints: 15168 sinusoidal: 5826 harmonic: 9342 Sorted by residual: dihedral pdb=" CB CYS C 329 " pdb=" SG CYS C 329 " pdb=" SG CYS C 354 " pdb=" CB CYS C 354 " ideal model delta sinusoidal sigma weight residual -86.00 -176.50 90.50 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS A 329 " pdb=" SG CYS A 329 " pdb=" SG CYS A 354 " pdb=" CB CYS A 354 " ideal model delta sinusoidal sigma weight residual -86.00 -176.48 90.48 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS B 329 " pdb=" SG CYS B 329 " pdb=" SG CYS B 354 " pdb=" CB CYS B 354 " ideal model delta sinusoidal sigma weight residual -86.00 -176.47 90.47 1 1.00e+01 1.00e-02 9.68e+01 ... (remaining 15165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2752 0.095 - 0.191: 984 0.191 - 0.286: 149 0.286 - 0.381: 12 0.381 - 0.476: 9 Chirality restraints: 3906 Sorted by residual: chirality pdb=" CA TRP A 536 " pdb=" N TRP A 536 " pdb=" C TRP A 536 " pdb=" CB TRP A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.68e+00 chirality pdb=" CA TRP B 536 " pdb=" N TRP B 536 " pdb=" C TRP B 536 " pdb=" CB TRP B 536 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CA TRP C 536 " pdb=" N TRP C 536 " pdb=" C TRP C 536 " pdb=" CB TRP C 536 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 3903 not shown) Planarity restraints: 4512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 751 " 0.065 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO C 752 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO C 752 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 752 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 751 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 752 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 752 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 752 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 751 " -0.065 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO B 752 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 752 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 752 " -0.053 5.00e-02 4.00e+02 ... (remaining 4509 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 10352 2.88 - 3.39: 23924 3.39 - 3.89: 43041 3.89 - 4.40: 51037 4.40 - 4.90: 79886 Nonbonded interactions: 208240 Sorted by model distance: nonbonded pdb=" O PHE B 371 " pdb=" SG CYS B 372 " model vdw 2.379 3.400 nonbonded pdb=" O PHE C 371 " pdb=" SG CYS C 372 " model vdw 2.380 3.400 nonbonded pdb=" O PHE A 371 " pdb=" SG CYS A 372 " model vdw 2.380 3.400 nonbonded pdb=" N TYR A 709 " pdb=" N SER A 710 " model vdw 2.393 2.560 nonbonded pdb=" N TYR C 709 " pdb=" N SER C 710 " model vdw 2.393 2.560 ... (remaining 208235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.170 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 64.320 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 : 0.018 0.150 25374 Z= 1.167 Angle : 1.834 17.156 34569 Z= 1.244 Chirality : 0.094 0.476 3906 Planarity : 0.010 0.101 4512 Dihedral : 9.753 89.544 9021 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.17 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3189 helix: 0.12 (0.17), residues: 843 sheet: 0.11 (0.21), residues: 567 loop : -0.95 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP B 536 HIS 0.007 0.002 HIS A1098 PHE 0.044 0.007 PHE C 123 TYR 0.042 0.009 TYR A 58 ARG 0.007 0.001 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 801 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 CYS cc_start: 0.5014 (t) cc_final: 0.4740 (t) REVERT: A 416 TYR cc_start: 0.8273 (t80) cc_final: 0.7810 (t80) REVERT: A 447 ASN cc_start: 0.7086 (t0) cc_final: 0.6477 (t0) REVERT: A 633 CYS cc_start: 0.5191 (m) cc_final: 0.4826 (m) REVERT: A 928 THR cc_start: 0.9312 (p) cc_final: 0.9008 (t) REVERT: A 1018 ASN cc_start: 0.8806 (t0) cc_final: 0.8406 (t0) REVERT: A 1024 SER cc_start: 0.9360 (t) cc_final: 0.9092 (m) REVERT: B 220 LYS cc_start: 0.8360 (mttt) cc_final: 0.8094 (ttpp) REVERT: B 240 TYR cc_start: 0.4986 (t80) cc_final: 0.4634 (t80) REVERT: B 361 LEU cc_start: 0.8735 (mt) cc_final: 0.8527 (tt) REVERT: B 446 TRP cc_start: 0.3453 (t-100) cc_final: 0.0718 (t-100) REVERT: B 447 ASN cc_start: 0.7123 (t0) cc_final: 0.6884 (t0) REVERT: B 485 ASP cc_start: 0.5412 (m-30) cc_final: 0.5173 (m-30) REVERT: B 633 CYS cc_start: 0.4594 (m) cc_final: 0.4105 (m) REVERT: B 928 THR cc_start: 0.9112 (p) cc_final: 0.8771 (t) REVERT: B 971 LYS cc_start: 0.7659 (mttp) cc_final: 0.7456 (tppt) REVERT: B 1018 ASN cc_start: 0.8877 (t0) cc_final: 0.8157 (m-40) REVERT: B 1024 SER cc_start: 0.9295 (t) cc_final: 0.9061 (m) REVERT: C 99 GLN cc_start: 0.5904 (mm-40) cc_final: 0.5460 (mp10) REVERT: C 136 SER cc_start: 0.6653 (t) cc_final: 0.6431 (p) REVERT: C 162 TYR cc_start: 0.5141 (p90) cc_final: 0.4872 (p90) REVERT: C 287 SER cc_start: 0.8510 (p) cc_final: 0.8016 (m) REVERT: C 299 MET cc_start: 0.7622 (mmp) cc_final: 0.7319 (mmm) REVERT: C 361 LEU cc_start: 0.8659 (mt) cc_final: 0.8386 (tt) REVERT: C 423 THR cc_start: 0.8936 (m) cc_final: 0.8593 (p) REVERT: C 446 TRP cc_start: 0.3087 (t-100) cc_final: 0.0311 (t-100) REVERT: C 613 ASN cc_start: 0.7647 (m-40) cc_final: 0.7299 (m-40) REVERT: C 698 ASP cc_start: 0.7379 (t0) cc_final: 0.7032 (t0) REVERT: C 928 THR cc_start: 0.9264 (p) cc_final: 0.9026 (t) REVERT: C 1018 ASN cc_start: 0.9123 (t0) cc_final: 0.8313 (m-40) REVERT: C 1076 ILE cc_start: 0.8907 (mt) cc_final: 0.8587 (mm) REVERT: C 1099 ILE cc_start: 0.8530 (mm) cc_final: 0.8283 (mm) outliers start: 0 outliers final: 0 residues processed: 801 average time/residue: 0.3844 time to fit residues: 466.4294 Evaluate side-chains 394 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 394 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 3.9990 chunk 241 optimal weight: 0.7980 chunk 133 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 151 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 288 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 192 ASN A 357 ASN A 426 GLN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS A 502 ASN A 613 ASN A 759 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN B 357 ASN B 441 HIS B 502 ASN B 606 GLN B 613 ASN B 696 ASN B 759 HIS ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 ASN B1061 GLN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN C 357 ASN C 441 HIS C 502 ASN C 696 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1061 GLN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 25374 Z= 0.275 Angle : 0.770 9.509 34569 Z= 0.430 Chirality : 0.048 0.209 3906 Planarity : 0.006 0.062 4512 Dihedral : 6.233 37.979 3486 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.05 % Allowed : 7.15 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3189 helix: 1.34 (0.18), residues: 864 sheet: 0.53 (0.22), residues: 525 loop : -0.98 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 346 HIS 0.008 0.002 HIS C1098 PHE 0.037 0.003 PHE B 500 TYR 0.036 0.002 TYR A 954 ARG 0.008 0.001 ARG A 955 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 426 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 TYR cc_start: 0.6430 (m-80) cc_final: 0.6212 (m-10) REVERT: A 294 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.7157 (m) REVERT: A 353 ASN cc_start: 0.8462 (m-40) cc_final: 0.7700 (p0) REVERT: A 364 TYR cc_start: 0.5868 (m-10) cc_final: 0.5641 (m-10) REVERT: A 384 CYS cc_start: 0.5907 (t) cc_final: 0.5496 (t) REVERT: A 824 GLN cc_start: 0.8256 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 898 GLN cc_start: 0.6544 (mm-40) cc_final: 0.6062 (mp10) REVERT: A 954 TYR cc_start: 0.7220 (m-80) cc_final: 0.6488 (m-80) REVERT: A 957 ASN cc_start: 0.7922 (m110) cc_final: 0.7413 (p0) REVERT: A 963 MET cc_start: 0.6077 (pmm) cc_final: 0.5829 (tpt) REVERT: A 1024 SER cc_start: 0.9333 (t) cc_final: 0.9122 (m) REVERT: B 191 ARG cc_start: 0.7610 (ttm170) cc_final: 0.7133 (ttm170) REVERT: B 220 LYS cc_start: 0.8361 (mttt) cc_final: 0.8141 (ttpp) REVERT: B 240 TYR cc_start: 0.5288 (t80) cc_final: 0.4765 (t80) REVERT: B 299 MET cc_start: 0.7567 (mmp) cc_final: 0.7223 (mmt) REVERT: B 353 ASN cc_start: 0.8136 (m-40) cc_final: 0.7214 (p0) REVERT: B 364 TYR cc_start: 0.5989 (m-10) cc_final: 0.5674 (m-10) REVERT: B 423 THR cc_start: 0.9274 (m) cc_final: 0.8811 (p) REVERT: B 921 GLU cc_start: 0.8305 (mp0) cc_final: 0.7996 (mp0) REVERT: B 963 MET cc_start: 0.5919 (pmm) cc_final: 0.5513 (tpt) REVERT: B 971 LYS cc_start: 0.7781 (mttp) cc_final: 0.7359 (tppt) REVERT: C 69 TYR cc_start: 0.8921 (m-80) cc_final: 0.8199 (m-80) REVERT: C 99 GLN cc_start: 0.5874 (mm-40) cc_final: 0.5391 (mp10) REVERT: C 149 MET cc_start: 0.7227 (mmt) cc_final: 0.6694 (mmt) REVERT: C 191 ARG cc_start: 0.6397 (ttm-80) cc_final: 0.5806 (tmm-80) REVERT: C 203 TYR cc_start: 0.6778 (m-80) cc_final: 0.6115 (m-10) REVERT: C 287 SER cc_start: 0.8730 (p) cc_final: 0.8362 (m) REVERT: C 294 CYS cc_start: 0.6806 (OUTLIER) cc_final: 0.6376 (m) REVERT: C 299 MET cc_start: 0.7513 (mmp) cc_final: 0.7148 (mmm) REVERT: C 353 ASN cc_start: 0.8352 (m-40) cc_final: 0.7372 (p0) REVERT: C 416 TYR cc_start: 0.7996 (t80) cc_final: 0.7622 (t80) REVERT: C 423 THR cc_start: 0.9284 (m) cc_final: 0.8689 (p) REVERT: C 734 MET cc_start: -0.0724 (mmt) cc_final: -0.1014 (mmt) REVERT: C 884 ASP cc_start: 0.6375 (t0) cc_final: 0.6136 (t0) REVERT: C 1076 ILE cc_start: 0.8730 (mt) cc_final: 0.8191 (mm) outliers start: 84 outliers final: 48 residues processed: 479 average time/residue: 0.3409 time to fit residues: 261.4366 Evaluate side-chains 381 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 331 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 607 THR Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 747 TYR Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 289 optimal weight: 0.9980 chunk 312 optimal weight: 0.9980 chunk 257 optimal weight: 0.0370 chunk 286 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 HIS ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN A 696 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN B 506 HIS ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1018 ASN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 25374 Z= 0.230 Angle : 0.663 11.689 34569 Z= 0.364 Chirality : 0.045 0.241 3906 Planarity : 0.005 0.055 4512 Dihedral : 6.048 38.006 3486 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.98 % Allowed : 9.62 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.15), residues: 3189 helix: 1.60 (0.18), residues: 894 sheet: 0.41 (0.22), residues: 534 loop : -1.11 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 178 HIS 0.006 0.001 HIS B1098 PHE 0.027 0.002 PHE B 500 TYR 0.029 0.002 TYR A 954 ARG 0.010 0.001 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 368 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 ASN cc_start: 0.8674 (m-40) cc_final: 0.7892 (p0) REVERT: A 366 GLN cc_start: 0.7821 (mt0) cc_final: 0.6791 (tp40) REVERT: A 749 MET cc_start: 0.5594 (mmt) cc_final: 0.5310 (mmm) REVERT: A 751 ILE cc_start: 0.6112 (mm) cc_final: 0.5855 (tt) REVERT: A 950 LEU cc_start: 0.7226 (tp) cc_final: 0.7020 (tp) REVERT: A 954 TYR cc_start: 0.7389 (m-80) cc_final: 0.6710 (m-80) REVERT: A 1018 ASN cc_start: 0.8817 (t0) cc_final: 0.8003 (t0) REVERT: A 1024 SER cc_start: 0.9376 (t) cc_final: 0.9068 (m) REVERT: B 41 THR cc_start: 0.7471 (p) cc_final: 0.7175 (t) REVERT: B 92 PHE cc_start: 0.6352 (m-80) cc_final: 0.5461 (m-10) REVERT: B 149 MET cc_start: 0.7099 (mmt) cc_final: 0.6622 (mtp) REVERT: B 191 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7478 (ttm-80) REVERT: B 220 LYS cc_start: 0.8441 (mttt) cc_final: 0.8202 (ttpp) REVERT: B 240 TYR cc_start: 0.5600 (t80) cc_final: 0.4689 (t80) REVERT: B 353 ASN cc_start: 0.8350 (m-40) cc_final: 0.7497 (p0) REVERT: B 423 THR cc_start: 0.9353 (m) cc_final: 0.9117 (p) REVERT: B 446 TRP cc_start: 0.4355 (t-100) cc_final: 0.1518 (t-100) REVERT: B 613 ASN cc_start: 0.6801 (t0) cc_final: 0.6024 (t0) REVERT: B 963 MET cc_start: 0.5785 (pmm) cc_final: 0.5246 (tpt) REVERT: B 971 LYS cc_start: 0.7660 (mttp) cc_final: 0.7333 (tppt) REVERT: C 99 GLN cc_start: 0.5991 (mm-40) cc_final: 0.5610 (mp10) REVERT: C 287 SER cc_start: 0.8913 (p) cc_final: 0.8614 (m) REVERT: C 299 MET cc_start: 0.7515 (mmp) cc_final: 0.7280 (mmm) REVERT: C 353 ASN cc_start: 0.8369 (m-40) cc_final: 0.7661 (p0) REVERT: C 416 TYR cc_start: 0.8043 (t80) cc_final: 0.7796 (t80) REVERT: C 423 THR cc_start: 0.9374 (m) cc_final: 0.8736 (p) REVERT: C 883 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8128 (p) REVERT: C 963 MET cc_start: 0.6288 (tpt) cc_final: 0.4675 (pmm) REVERT: C 1076 ILE cc_start: 0.8558 (mt) cc_final: 0.8162 (mm) outliers start: 82 outliers final: 63 residues processed: 419 average time/residue: 0.3438 time to fit residues: 235.4988 Evaluate side-chains 368 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 304 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 940 TRP Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 706 CYS Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 883 SER Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 0.9980 chunk 217 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 290 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 275 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 GLN B1080 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1005 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25374 Z= 0.277 Angle : 0.673 8.589 34569 Z= 0.365 Chirality : 0.046 0.211 3906 Planarity : 0.005 0.059 4512 Dihedral : 6.038 38.048 3486 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.14 % Allowed : 10.28 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.15), residues: 3189 helix: 1.56 (0.18), residues: 894 sheet: 0.11 (0.21), residues: 552 loop : -1.24 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 178 HIS 0.008 0.001 HIS B1098 PHE 0.028 0.002 PHE B 642 TYR 0.024 0.002 TYR A 416 ARG 0.007 0.001 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 337 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.6463 (mm-40) cc_final: 0.6039 (mp10) REVERT: A 191 ARG cc_start: 0.7792 (ttm170) cc_final: 0.7473 (ttp-110) REVERT: A 294 CYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6924 (m) REVERT: A 353 ASN cc_start: 0.8719 (m-40) cc_final: 0.8002 (p0) REVERT: A 416 TYR cc_start: 0.7639 (t80) cc_final: 0.7384 (t80) REVERT: A 613 ASN cc_start: 0.7355 (t0) cc_final: 0.7125 (t0) REVERT: A 671 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7248 (m-40) REVERT: A 749 MET cc_start: 0.5230 (mmt) cc_final: 0.5025 (mmm) REVERT: A 914 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8691 (p) REVERT: A 950 LEU cc_start: 0.7382 (tp) cc_final: 0.6934 (tp) REVERT: A 954 TYR cc_start: 0.7536 (m-80) cc_final: 0.6804 (m-80) REVERT: A 970 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 971 LYS cc_start: 0.7729 (tppt) cc_final: 0.7073 (mttp) REVERT: A 1018 ASN cc_start: 0.8893 (t0) cc_final: 0.7951 (t0) REVERT: A 1024 SER cc_start: 0.9375 (t) cc_final: 0.9128 (m) REVERT: A 1091 ASN cc_start: 0.7746 (m-40) cc_final: 0.7538 (t0) REVERT: B 41 THR cc_start: 0.7465 (p) cc_final: 0.7154 (t) REVERT: B 191 ARG cc_start: 0.7634 (ttm170) cc_final: 0.7337 (ttm170) REVERT: B 220 LYS cc_start: 0.8446 (mttt) cc_final: 0.8174 (pttt) REVERT: B 240 TYR cc_start: 0.5381 (t80) cc_final: 0.5078 (t80) REVERT: B 353 ASN cc_start: 0.8400 (m-40) cc_final: 0.7729 (p0) REVERT: B 595 LYS cc_start: 0.7825 (tptm) cc_final: 0.7564 (mttp) REVERT: B 638 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8066 (t) REVERT: B 899 GLU cc_start: 0.7384 (tp30) cc_final: 0.7134 (tp30) REVERT: B 971 LYS cc_start: 0.7800 (mttp) cc_final: 0.7539 (tppt) REVERT: C 92 PHE cc_start: 0.5463 (m-80) cc_final: 0.4261 (m-10) REVERT: C 294 CYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6537 (m) REVERT: C 299 MET cc_start: 0.7607 (mmp) cc_final: 0.7303 (mmm) REVERT: C 353 ASN cc_start: 0.8426 (m-40) cc_final: 0.7776 (p0) REVERT: C 370 LEU cc_start: 0.8853 (tp) cc_final: 0.8581 (tt) REVERT: C 416 TYR cc_start: 0.8091 (t80) cc_final: 0.7771 (t80) REVERT: C 423 THR cc_start: 0.9277 (m) cc_final: 0.8621 (p) REVERT: C 883 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8242 (t) REVERT: C 898 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: C 963 MET cc_start: 0.6474 (tpt) cc_final: 0.4628 (pmm) REVERT: C 1018 ASN cc_start: 0.8930 (t0) cc_final: 0.8204 (t0) REVERT: C 1076 ILE cc_start: 0.8588 (mt) cc_final: 0.8329 (mm) outliers start: 114 outliers final: 71 residues processed: 418 average time/residue: 0.3510 time to fit residues: 239.0920 Evaluate side-chains 379 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 301 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 883 SER Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1103 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 126 optimal weight: 0.5980 chunk 262 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 156 optimal weight: 0.6980 chunk 275 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 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 366 GLN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25374 Z= 0.212 Angle : 0.627 8.682 34569 Z= 0.339 Chirality : 0.044 0.220 3906 Planarity : 0.004 0.051 4512 Dihedral : 5.854 37.161 3486 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.92 % Allowed : 10.89 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.15), residues: 3189 helix: 1.77 (0.18), residues: 888 sheet: 0.11 (0.21), residues: 552 loop : -1.22 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 334 HIS 0.008 0.001 HIS C 716 PHE 0.025 0.002 PHE C 385 TYR 0.021 0.002 TYR A 450 ARG 0.011 0.001 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 324 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.4980 (m-80) cc_final: 0.4569 (m-10) REVERT: A 99 GLN cc_start: 0.6486 (mm-40) cc_final: 0.6034 (mp10) REVERT: A 191 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7469 (ttp-110) REVERT: A 294 CYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6842 (m) REVERT: A 353 ASN cc_start: 0.8698 (m-40) cc_final: 0.7930 (p0) REVERT: A 574 GLU cc_start: 0.7854 (pp20) cc_final: 0.7146 (mp0) REVERT: A 613 ASN cc_start: 0.7340 (t0) cc_final: 0.7135 (t0) REVERT: A 671 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7511 (m-40) REVERT: A 749 MET cc_start: 0.5427 (mmt) cc_final: 0.5219 (mmm) REVERT: A 950 LEU cc_start: 0.7342 (tp) cc_final: 0.6789 (tp) REVERT: A 954 TYR cc_start: 0.7926 (m-80) cc_final: 0.7265 (m-80) REVERT: A 963 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.3220 (pmm) REVERT: A 1018 ASN cc_start: 0.8762 (t0) cc_final: 0.7912 (t0) REVERT: A 1024 SER cc_start: 0.9374 (t) cc_final: 0.9027 (m) REVERT: B 191 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7290 (ttm170) REVERT: B 220 LYS cc_start: 0.8471 (mttt) cc_final: 0.8153 (pttt) REVERT: B 240 TYR cc_start: 0.5452 (t80) cc_final: 0.5104 (t80) REVERT: B 353 ASN cc_start: 0.8395 (m-40) cc_final: 0.7645 (p0) REVERT: B 574 GLU cc_start: 0.7801 (pp20) cc_final: 0.7037 (mp0) REVERT: B 904 LEU cc_start: 0.8546 (mm) cc_final: 0.8085 (mm) REVERT: B 957 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.8001 (p0) REVERT: B 963 MET cc_start: 0.5292 (pmm) cc_final: 0.4978 (tpt) REVERT: B 971 LYS cc_start: 0.7765 (mttp) cc_final: 0.7491 (tppt) REVERT: C 92 PHE cc_start: 0.4841 (m-80) cc_final: 0.4441 (m-10) REVERT: C 294 CYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6479 (m) REVERT: C 299 MET cc_start: 0.7573 (mmp) cc_final: 0.7218 (mmm) REVERT: C 326 LEU cc_start: 0.6540 (mt) cc_final: 0.6239 (mp) REVERT: C 353 ASN cc_start: 0.8430 (m-40) cc_final: 0.8111 (t0) REVERT: C 370 LEU cc_start: 0.8890 (tp) cc_final: 0.8575 (tt) REVERT: C 416 TYR cc_start: 0.8074 (t80) cc_final: 0.7772 (t80) REVERT: C 423 THR cc_start: 0.9283 (m) cc_final: 0.8698 (p) REVERT: C 898 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: C 963 MET cc_start: 0.6668 (tpt) cc_final: 0.4773 (pmm) REVERT: C 1018 ASN cc_start: 0.8867 (t0) cc_final: 0.8114 (t0) REVERT: C 1076 ILE cc_start: 0.8546 (mt) cc_final: 0.8246 (mm) outliers start: 108 outliers final: 76 residues processed: 404 average time/residue: 0.3123 time to fit residues: 206.5684 Evaluate side-chains 371 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 289 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 635 SER Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 883 SER Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 957 ASN Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 307 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 985 GLN C 999 GLN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25374 Z= 0.269 Angle : 0.654 9.451 34569 Z= 0.352 Chirality : 0.045 0.211 3906 Planarity : 0.005 0.054 4512 Dihedral : 5.840 36.419 3486 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.54 % Allowed : 11.33 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3189 helix: 1.56 (0.18), residues: 897 sheet: -0.01 (0.20), residues: 582 loop : -1.31 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 536 HIS 0.007 0.001 HIS B1098 PHE 0.023 0.002 PHE B 371 TYR 0.022 0.002 TYR A 416 ARG 0.010 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 315 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.5453 (m-80) cc_final: 0.4935 (m-10) REVERT: A 99 GLN cc_start: 0.6575 (mm-40) cc_final: 0.6033 (mp10) REVERT: A 137 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6560 (t80) REVERT: A 191 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7126 (ttm170) REVERT: A 294 CYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6916 (m) REVERT: A 574 GLU cc_start: 0.7850 (pp20) cc_final: 0.7173 (mp0) REVERT: A 671 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7131 (m-40) REVERT: A 749 MET cc_start: 0.5294 (mmt) cc_final: 0.5084 (mmm) REVERT: A 950 LEU cc_start: 0.7451 (tp) cc_final: 0.6789 (tp) REVERT: A 954 TYR cc_start: 0.7966 (m-80) cc_final: 0.7288 (m-80) REVERT: A 963 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.3636 (pmm) REVERT: A 1018 ASN cc_start: 0.8854 (t0) cc_final: 0.8030 (t0) REVERT: A 1024 SER cc_start: 0.9449 (t) cc_final: 0.9062 (m) REVERT: A 1117 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7232 (p90) REVERT: B 149 MET cc_start: 0.7333 (mmt) cc_final: 0.6742 (mtp) REVERT: B 191 ARG cc_start: 0.7368 (ttm170) cc_final: 0.7057 (ttm170) REVERT: B 220 LYS cc_start: 0.8526 (mttt) cc_final: 0.8167 (pttt) REVERT: B 240 TYR cc_start: 0.5410 (t80) cc_final: 0.5104 (t80) REVERT: B 353 ASN cc_start: 0.8375 (m-40) cc_final: 0.7541 (p0) REVERT: B 574 GLU cc_start: 0.7891 (pp20) cc_final: 0.7287 (mp0) REVERT: B 638 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8037 (t) REVERT: B 963 MET cc_start: 0.5870 (pmm) cc_final: 0.5250 (tpt) REVERT: B 971 LYS cc_start: 0.7684 (mttp) cc_final: 0.7113 (tppt) REVERT: C 92 PHE cc_start: 0.4874 (m-80) cc_final: 0.4519 (m-10) REVERT: C 294 CYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6457 (m) REVERT: C 299 MET cc_start: 0.7694 (mmp) cc_final: 0.7416 (mmm) REVERT: C 353 ASN cc_start: 0.8431 (m-40) cc_final: 0.7709 (p0) REVERT: C 370 LEU cc_start: 0.8948 (tp) cc_final: 0.8621 (tt) REVERT: C 416 TYR cc_start: 0.8124 (t80) cc_final: 0.7770 (t80) REVERT: C 472 PHE cc_start: 0.3815 (m-80) cc_final: 0.3369 (m-80) REVERT: C 898 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: C 936 MET cc_start: 0.7302 (mtt) cc_final: 0.6667 (mtt) REVERT: C 948 PHE cc_start: 0.6610 (t80) cc_final: 0.5447 (t80) REVERT: C 963 MET cc_start: 0.6219 (tpt) cc_final: 0.4151 (pmm) REVERT: C 1018 ASN cc_start: 0.8995 (t0) cc_final: 0.8191 (t0) REVERT: C 1076 ILE cc_start: 0.8647 (mt) cc_final: 0.8358 (mm) outliers start: 125 outliers final: 87 residues processed: 408 average time/residue: 0.3283 time to fit residues: 218.6790 Evaluate side-chains 385 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 290 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 676 PHE Chi-restraints excluded: chain A residue 716 HIS Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 963 MET Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 818 VAL Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 929 THR Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 716 HIS Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 866 ILE Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 175 optimal weight: 0.0870 chunk 224 optimal weight: 0.0370 chunk 174 optimal weight: 0.6980 chunk 259 optimal weight: 8.9990 chunk 171 optimal weight: 0.0980 chunk 306 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 716 HIS ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.5351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25374 Z= 0.185 Angle : 0.610 9.463 34569 Z= 0.330 Chirality : 0.044 0.212 3906 Planarity : 0.004 0.053 4512 Dihedral : 5.638 35.206 3486 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.27 % Allowed : 13.18 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.15), residues: 3189 helix: 1.61 (0.18), residues: 906 sheet: -0.02 (0.20), residues: 594 loop : -1.19 (0.16), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 536 HIS 0.004 0.001 HIS C1098 PHE 0.027 0.002 PHE C 371 TYR 0.020 0.001 TYR A 416 ARG 0.007 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 329 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.5456 (m-80) cc_final: 0.4912 (m-10) REVERT: A 99 GLN cc_start: 0.6474 (mm-40) cc_final: 0.5991 (mp10) REVERT: A 137 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.6805 (t80) REVERT: A 191 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7244 (ttm170) REVERT: A 294 CYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6865 (m) REVERT: A 574 GLU cc_start: 0.7830 (pp20) cc_final: 0.7190 (mp0) REVERT: A 628 TYR cc_start: 0.8507 (m-80) cc_final: 0.8233 (m-80) REVERT: A 664 ASN cc_start: 0.8224 (m-40) cc_final: 0.7672 (t0) REVERT: A 950 LEU cc_start: 0.7423 (tp) cc_final: 0.6718 (tp) REVERT: A 954 TYR cc_start: 0.7917 (m-80) cc_final: 0.7267 (m-80) REVERT: A 963 MET cc_start: 0.5657 (tpt) cc_final: 0.3218 (pmm) REVERT: A 1018 ASN cc_start: 0.8565 (t0) cc_final: 0.7897 (t0) REVERT: A 1024 SER cc_start: 0.9389 (t) cc_final: 0.8983 (m) REVERT: A 1117 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.7117 (p90) REVERT: B 149 MET cc_start: 0.7272 (mmt) cc_final: 0.6704 (mtp) REVERT: B 191 ARG cc_start: 0.7251 (ttm170) cc_final: 0.6885 (ttm170) REVERT: B 220 LYS cc_start: 0.8506 (mttt) cc_final: 0.8094 (ttpp) REVERT: B 240 TYR cc_start: 0.5361 (t80) cc_final: 0.5068 (t80) REVERT: B 334 TRP cc_start: 0.7861 (t60) cc_final: 0.7487 (t60) REVERT: B 353 ASN cc_start: 0.8433 (m-40) cc_final: 0.7521 (p0) REVERT: B 383 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7423 (mmm160) REVERT: B 574 GLU cc_start: 0.7642 (pp20) cc_final: 0.6973 (mp0) REVERT: B 612 VAL cc_start: 0.8685 (m) cc_final: 0.8468 (p) REVERT: B 957 ASN cc_start: 0.8367 (p0) cc_final: 0.7471 (m-40) REVERT: B 963 MET cc_start: 0.5824 (pmm) cc_final: 0.5258 (tpt) REVERT: B 971 LYS cc_start: 0.7672 (mttp) cc_final: 0.7306 (tppt) REVERT: C 92 PHE cc_start: 0.4892 (m-80) cc_final: 0.4564 (m-10) REVERT: C 294 CYS cc_start: 0.6660 (OUTLIER) cc_final: 0.6364 (m) REVERT: C 299 MET cc_start: 0.7678 (mmp) cc_final: 0.7362 (mmm) REVERT: C 330 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7225 (p0) REVERT: C 352 GLN cc_start: 0.7693 (mt0) cc_final: 0.7194 (mt0) REVERT: C 353 ASN cc_start: 0.8352 (m-40) cc_final: 0.7199 (p0) REVERT: C 370 LEU cc_start: 0.8911 (tp) cc_final: 0.8566 (tt) REVERT: C 416 TYR cc_start: 0.8104 (t80) cc_final: 0.7747 (t80) REVERT: C 734 MET cc_start: -0.2414 (mmt) cc_final: -0.2696 (mmt) REVERT: C 963 MET cc_start: 0.6149 (tpt) cc_final: 0.4091 (pmm) REVERT: C 1018 ASN cc_start: 0.8889 (t0) cc_final: 0.7969 (t0) REVERT: C 1076 ILE cc_start: 0.8728 (mt) cc_final: 0.8353 (mm) outliers start: 90 outliers final: 72 residues processed: 389 average time/residue: 0.3326 time to fit residues: 207.2388 Evaluate side-chains 378 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 301 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 407 ASN Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1092 PHE Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.3980 chunk 122 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 25374 Z= 0.252 Angle : 0.648 12.868 34569 Z= 0.348 Chirality : 0.045 0.213 3906 Planarity : 0.005 0.056 4512 Dihedral : 5.705 34.543 3486 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.52 % Allowed : 13.54 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3189 helix: 1.50 (0.18), residues: 906 sheet: -0.12 (0.20), residues: 612 loop : -1.25 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 91 HIS 0.007 0.001 HIS B1098 PHE 0.030 0.002 PHE C 371 TYR 0.022 0.002 TYR A 416 ARG 0.008 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 312 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.5478 (m-80) cc_final: 0.5274 (m-80) REVERT: A 99 GLN cc_start: 0.6620 (mm-40) cc_final: 0.6014 (mp10) REVERT: A 137 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6707 (t80) REVERT: A 191 ARG cc_start: 0.7686 (ttm170) cc_final: 0.7170 (ttm170) REVERT: A 294 CYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6922 (m) REVERT: A 313 VAL cc_start: 0.8596 (t) cc_final: 0.8366 (p) REVERT: A 450 TYR cc_start: 0.7500 (p90) cc_final: 0.7195 (p90) REVERT: A 574 GLU cc_start: 0.7886 (pp20) cc_final: 0.7253 (mp0) REVERT: A 628 TYR cc_start: 0.8490 (m-80) cc_final: 0.8152 (m-80) REVERT: A 671 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7145 (m-40) REVERT: A 950 LEU cc_start: 0.7487 (tp) cc_final: 0.6698 (tp) REVERT: A 954 TYR cc_start: 0.7933 (m-80) cc_final: 0.7219 (m-80) REVERT: A 963 MET cc_start: 0.6158 (tpt) cc_final: 0.3755 (pmm) REVERT: A 1018 ASN cc_start: 0.8930 (t0) cc_final: 0.8122 (t0) REVERT: A 1024 SER cc_start: 0.9425 (t) cc_final: 0.9019 (m) REVERT: A 1117 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7071 (p90) REVERT: B 149 MET cc_start: 0.7339 (mmt) cc_final: 0.6749 (mtp) REVERT: B 191 ARG cc_start: 0.7295 (ttm170) cc_final: 0.6840 (ttm170) REVERT: B 220 LYS cc_start: 0.8605 (mttt) cc_final: 0.8306 (ttpt) REVERT: B 240 TYR cc_start: 0.5432 (t80) cc_final: 0.5213 (t80) REVERT: B 353 ASN cc_start: 0.8355 (m-40) cc_final: 0.7662 (p0) REVERT: B 574 GLU cc_start: 0.7745 (pp20) cc_final: 0.6943 (mp0) REVERT: B 613 ASN cc_start: 0.7243 (t0) cc_final: 0.6834 (t0) REVERT: B 638 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8250 (t) REVERT: B 814 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.6665 (mmt) REVERT: B 963 MET cc_start: 0.6005 (pmm) cc_final: 0.5233 (tpt) REVERT: B 971 LYS cc_start: 0.7753 (mttp) cc_final: 0.7373 (tppt) REVERT: C 48 LEU cc_start: 0.8417 (tp) cc_final: 0.8195 (mp) REVERT: C 92 PHE cc_start: 0.5557 (m-80) cc_final: 0.5328 (m-10) REVERT: C 294 CYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6453 (m) REVERT: C 299 MET cc_start: 0.7739 (mmp) cc_final: 0.7373 (mmm) REVERT: C 370 LEU cc_start: 0.8945 (tp) cc_final: 0.8558 (tt) REVERT: C 376 ASP cc_start: 0.6851 (t70) cc_final: 0.6226 (t0) REVERT: C 734 MET cc_start: -0.2422 (mmt) cc_final: -0.2661 (mmt) REVERT: C 898 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7117 (mp10) REVERT: C 936 MET cc_start: 0.7708 (mtt) cc_final: 0.7323 (mmm) REVERT: C 948 PHE cc_start: 0.6418 (t80) cc_final: 0.5765 (t80) REVERT: C 963 MET cc_start: 0.6200 (tpt) cc_final: 0.4113 (pmm) REVERT: C 1018 ASN cc_start: 0.8987 (t0) cc_final: 0.8108 (t0) REVERT: C 1076 ILE cc_start: 0.8707 (mt) cc_final: 0.8337 (mm) outliers start: 97 outliers final: 80 residues processed: 379 average time/residue: 0.3479 time to fit residues: 211.7217 Evaluate side-chains 379 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 291 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 635 SER Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 898 GLN Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.9980 chunk 293 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 285 optimal weight: 0.9980 chunk 171 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 0.0470 chunk 284 optimal weight: 5.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN A 502 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1097 ASN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25374 Z= 0.207 Angle : 0.615 9.723 34569 Z= 0.330 Chirality : 0.043 0.181 3906 Planarity : 0.004 0.057 4512 Dihedral : 5.616 33.771 3486 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.34 % Allowed : 14.31 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.15), residues: 3189 helix: 1.55 (0.18), residues: 912 sheet: -0.07 (0.20), residues: 612 loop : -1.24 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 178 HIS 0.006 0.001 HIS B1098 PHE 0.028 0.002 PHE C 371 TYR 0.022 0.002 TYR A 416 ARG 0.007 0.000 ARG C 724 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 326 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.5442 (m-80) cc_final: 0.5214 (m-80) REVERT: A 99 GLN cc_start: 0.6364 (mm-40) cc_final: 0.6028 (mp10) REVERT: A 137 TYR cc_start: 0.7351 (OUTLIER) cc_final: 0.6333 (t80) REVERT: A 191 ARG cc_start: 0.7394 (ttm170) cc_final: 0.6950 (ttm170) REVERT: A 313 VAL cc_start: 0.8590 (t) cc_final: 0.8381 (p) REVERT: A 370 LEU cc_start: 0.8564 (tp) cc_final: 0.8210 (tt) REVERT: A 450 TYR cc_start: 0.7531 (p90) cc_final: 0.7240 (p90) REVERT: A 574 GLU cc_start: 0.7587 (pp20) cc_final: 0.7278 (mp0) REVERT: A 628 TYR cc_start: 0.8426 (m-80) cc_final: 0.8144 (m-80) REVERT: A 671 ASN cc_start: 0.7724 (OUTLIER) cc_final: 0.7073 (m-40) REVERT: A 936 MET cc_start: 0.7673 (mtp) cc_final: 0.7458 (mtp) REVERT: A 950 LEU cc_start: 0.7531 (tp) cc_final: 0.6714 (tp) REVERT: A 954 TYR cc_start: 0.7895 (m-80) cc_final: 0.7471 (m-80) REVERT: A 963 MET cc_start: 0.6061 (tpt) cc_final: 0.4025 (pmm) REVERT: A 971 LYS cc_start: 0.7648 (tppt) cc_final: 0.6524 (mtpt) REVERT: A 1018 ASN cc_start: 0.8782 (t0) cc_final: 0.7991 (t0) REVERT: A 1024 SER cc_start: 0.9413 (t) cc_final: 0.9020 (m) REVERT: A 1117 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.6980 (p90) REVERT: B 149 MET cc_start: 0.7339 (mmt) cc_final: 0.6742 (mtp) REVERT: B 191 ARG cc_start: 0.7210 (ttm170) cc_final: 0.6770 (ttm170) REVERT: B 220 LYS cc_start: 0.8570 (mttt) cc_final: 0.8254 (ttpt) REVERT: B 240 TYR cc_start: 0.5410 (t80) cc_final: 0.5115 (t80) REVERT: B 334 TRP cc_start: 0.7641 (t60) cc_final: 0.7282 (t60) REVERT: B 353 ASN cc_start: 0.8212 (m-40) cc_final: 0.7555 (p0) REVERT: B 574 GLU cc_start: 0.7765 (pp20) cc_final: 0.7080 (mp0) REVERT: B 613 ASN cc_start: 0.7296 (t0) cc_final: 0.6926 (t0) REVERT: B 645 ASP cc_start: 0.7359 (p0) cc_final: 0.6771 (p0) REVERT: B 814 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6642 (mmt) REVERT: B 957 ASN cc_start: 0.8308 (p0) cc_final: 0.7532 (m-40) REVERT: B 963 MET cc_start: 0.5824 (pmm) cc_final: 0.5105 (tpt) REVERT: C 164 ASP cc_start: 0.6949 (t0) cc_final: 0.6619 (t0) REVERT: C 294 CYS cc_start: 0.6719 (OUTLIER) cc_final: 0.6400 (m) REVERT: C 299 MET cc_start: 0.7729 (mmp) cc_final: 0.7374 (mmm) REVERT: C 370 LEU cc_start: 0.8906 (tp) cc_final: 0.8556 (tt) REVERT: C 734 MET cc_start: -0.2364 (mmt) cc_final: -0.2642 (mmt) REVERT: C 948 PHE cc_start: 0.6436 (t80) cc_final: 0.6017 (t80) REVERT: C 963 MET cc_start: 0.5578 (tpt) cc_final: 0.3978 (pmm) REVERT: C 1018 ASN cc_start: 0.8922 (t0) cc_final: 0.8005 (t0) REVERT: C 1076 ILE cc_start: 0.8671 (mt) cc_final: 0.8306 (mm) outliers start: 92 outliers final: 80 residues processed: 387 average time/residue: 0.3322 time to fit residues: 206.2621 Evaluate side-chains 370 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 285 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain B residue 1092 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 479 CYS Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.7980 chunk 302 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 chunk 154 optimal weight: 7.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25374 Z= 0.222 Angle : 0.630 11.060 34569 Z= 0.338 Chirality : 0.044 0.181 3906 Planarity : 0.004 0.062 4512 Dihedral : 5.650 36.758 3486 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.71 % Favored : 92.25 % Rotamer: Outliers : 3.23 % Allowed : 14.89 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3189 helix: 1.52 (0.18), residues: 912 sheet: -0.00 (0.20), residues: 606 loop : -1.29 (0.16), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 178 HIS 0.007 0.001 HIS B1098 PHE 0.033 0.002 PHE C 550 TYR 0.025 0.002 TYR B 416 ARG 0.008 0.000 ARG C 724 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6378 Ramachandran restraints generated. 3189 Oldfield, 0 Emsley, 3189 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 294 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.5453 (m-80) cc_final: 0.5207 (m-80) REVERT: A 99 GLN cc_start: 0.6283 (mm-40) cc_final: 0.5847 (mp10) REVERT: A 137 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6450 (t80) REVERT: A 191 ARG cc_start: 0.7357 (ttm170) cc_final: 0.7078 (ptm160) REVERT: A 294 CYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6912 (m) REVERT: A 370 LEU cc_start: 0.8556 (tp) cc_final: 0.8199 (tt) REVERT: A 574 GLU cc_start: 0.7584 (pp20) cc_final: 0.7145 (mp0) REVERT: A 628 TYR cc_start: 0.8052 (m-80) cc_final: 0.7769 (m-80) REVERT: A 671 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7067 (m-40) REVERT: A 1018 ASN cc_start: 0.8890 (t0) cc_final: 0.8062 (t0) REVERT: A 1024 SER cc_start: 0.9407 (t) cc_final: 0.9012 (m) REVERT: A 1117 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7000 (p90) REVERT: B 92 PHE cc_start: 0.6473 (m-80) cc_final: 0.5287 (m-10) REVERT: B 149 MET cc_start: 0.6905 (mmt) cc_final: 0.6403 (mtp) REVERT: B 191 ARG cc_start: 0.7133 (ttm170) cc_final: 0.6781 (ttm170) REVERT: B 220 LYS cc_start: 0.8629 (mttt) cc_final: 0.8319 (ttpt) REVERT: B 240 TYR cc_start: 0.5444 (t80) cc_final: 0.4775 (t80) REVERT: B 334 TRP cc_start: 0.7874 (t60) cc_final: 0.7477 (t60) REVERT: B 353 ASN cc_start: 0.8213 (m-40) cc_final: 0.7451 (p0) REVERT: B 613 ASN cc_start: 0.7363 (t0) cc_final: 0.7017 (t0) REVERT: B 645 ASP cc_start: 0.7389 (p0) cc_final: 0.6837 (p0) REVERT: B 814 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.6667 (mmt) REVERT: B 957 ASN cc_start: 0.8299 (p0) cc_final: 0.7534 (m-40) REVERT: B 963 MET cc_start: 0.5823 (pmm) cc_final: 0.4956 (tpt) REVERT: C 149 MET cc_start: 0.6975 (mtm) cc_final: 0.6718 (mtt) REVERT: C 164 ASP cc_start: 0.7009 (t0) cc_final: 0.6705 (t0) REVERT: C 191 ARG cc_start: 0.7173 (ptm160) cc_final: 0.6689 (ptm160) REVERT: C 294 CYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6422 (m) REVERT: C 299 MET cc_start: 0.7549 (mmp) cc_final: 0.7218 (mmm) REVERT: C 370 LEU cc_start: 0.8725 (tp) cc_final: 0.8317 (tt) REVERT: C 734 MET cc_start: -0.2371 (mmt) cc_final: -0.2632 (mmt) REVERT: C 948 PHE cc_start: 0.6460 (t80) cc_final: 0.6109 (t80) REVERT: C 963 MET cc_start: 0.5583 (tpt) cc_final: 0.3952 (pmm) REVERT: C 1018 ASN cc_start: 0.9011 (t0) cc_final: 0.8135 (t0) REVERT: C 1076 ILE cc_start: 0.8675 (mt) cc_final: 0.8317 (mm) outliers start: 89 outliers final: 79 residues processed: 352 average time/residue: 0.3310 time to fit residues: 189.5223 Evaluate side-chains 368 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 283 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 137 TYR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 217 TYR Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 294 CYS Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 391 ASP Chi-restraints excluded: chain A residue 479 CYS Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 556 ASN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 627 THR Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 747 TYR Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1014 ASN Chi-restraints excluded: chain A residue 1064 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1088 THR Chi-restraints excluded: chain A residue 1103 VAL Chi-restraints excluded: chain A residue 1117 TYR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 375 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 479 CYS Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 534 ILE Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 867 ARG Chi-restraints excluded: chain B residue 902 ASP Chi-restraints excluded: chain B residue 904 LEU Chi-restraints excluded: chain B residue 937 PHE Chi-restraints excluded: chain B residue 940 TRP Chi-restraints excluded: chain B residue 1064 ASP Chi-restraints excluded: chain B residue 1088 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 217 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 294 CYS Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 391 ASP Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 902 ASP Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 940 TRP Chi-restraints excluded: chain C residue 1005 ASN Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1064 ASP Chi-restraints excluded: chain C residue 1088 THR Chi-restraints excluded: chain C residue 1103 VAL Chi-restraints excluded: chain C residue 1117 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.9980 chunk 268 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 252 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.186921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.180145 restraints weight = 40312.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.179314 restraints weight = 56074.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.177706 restraints weight = 60154.340| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25374 Z= 0.208 Angle : 0.631 12.446 34569 Z= 0.339 Chirality : 0.044 0.201 3906 Planarity : 0.004 0.057 4512 Dihedral : 5.546 32.593 3486 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.53 % Favored : 92.44 % Rotamer: Outliers : 3.16 % Allowed : 15.14 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 3189 helix: 1.56 (0.18), residues: 912 sheet: -0.01 (0.20), residues: 609 loop : -1.29 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 178 HIS 0.006 0.001 HIS C1098 PHE 0.037 0.002 PHE C 472 TYR 0.022 0.002 TYR A 416 ARG 0.008 0.000 ARG C 724 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4957.28 seconds wall clock time: 90 minutes 30.71 seconds (5430.71 seconds total)