Starting phenix.real_space_refine on Sun Nov 19 01:14:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/11_2023/3jcl_6526.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/11_2023/3jcl_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_6526/11_2023/3jcl_6526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/11_2023/3jcl_6526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/11_2023/3jcl_6526.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcl_6526/11_2023/3jcl_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 13.79, per 1000 atoms: 0.56 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: 10.41 Conformation dependent library (CDL) restraints added in 5.0 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: 3.81 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: 11.22 Time building geometry restraints manager: 11.14 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: 2.190 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: 6.390 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 73.290 Find NCS groups from input model: 1.410 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.570 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 801 average time/residue: 0.3917 time to fit residues: 476.7762 Evaluate side-chains 380 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 2.769 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8562 ------------------------------------------------------------------------------- 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: 0.6980 chunk 151 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 288 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 696 ASN A 759 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN 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 B1018 ASN B1061 GLN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 ASN C 357 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS C 502 ASN ** C 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 696 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN C1018 ASN C1061 GLN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 25374 Z= 0.291 Angle : 0.789 9.701 34569 Z= 0.439 Chirality : 0.048 0.215 3906 Planarity : 0.006 0.063 4512 Dihedral : 6.222 37.761 3486 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.23 % Allowed : 7.33 % Favored : 89.43 % 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: -0.18 (0.15), residues: 3189 helix: 1.27 (0.18), residues: 864 sheet: 0.47 (0.22), residues: 525 loop : -1.02 (0.14), residues: 1800 *********************** 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 501 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 412 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 50 residues processed: 468 average time/residue: 0.3524 time to fit residues: 264.2055 Evaluate side-chains 365 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 315 time to evaluate : 2.788 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.2863 time to fit residues: 28.7297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 289 optimal weight: 0.7980 chunk 312 optimal weight: 0.5980 chunk 257 optimal weight: 0.7980 chunk 286 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 232 optimal weight: 5.9990 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 98 ASN A 506 HIS ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN B 506 HIS ** 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 506 HIS C 613 ASN ** C 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 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: 0.7368 moved from start: 0.4000 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= 0.236 Angle : 0.681 11.749 34569 Z= 0.374 Chirality : 0.045 0.209 3906 Planarity : 0.005 0.056 4512 Dihedral : 6.072 38.369 3486 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.56 % Allowed : 10.82 % Favored : 87.62 % 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: -0.14 (0.15), residues: 3189 helix: 1.50 (0.18), residues: 894 sheet: 0.36 (0.22), residues: 534 loop : -1.12 (0.15), residues: 1761 *********************** 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 404 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 361 time to evaluate : 2.852 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 outliers start: 43 outliers final: 22 residues processed: 388 average time/residue: 0.3470 time to fit residues: 218.6307 Evaluate side-chains 313 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 291 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2238 time to fit residues: 13.0938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 138 optimal weight: 0.3980 chunk 194 optimal weight: 8.9990 chunk 290 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 275 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- 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** A1014 ASN A1018 ASN B 613 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN ** B 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 GLN B1080 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 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** ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 25374 Z= 0.273 Angle : 0.677 8.382 34569 Z= 0.368 Chirality : 0.046 0.201 3906 Planarity : 0.005 0.058 4512 Dihedral : 6.015 37.973 3486 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.29 % Allowed : 11.58 % Favored : 86.13 % 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: -0.26 (0.15), residues: 3189 helix: 1.54 (0.18), residues: 897 sheet: 0.06 (0.21), residues: 558 loop : -1.21 (0.15), residues: 1734 *********************** 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 392 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 329 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 27 residues processed: 369 average time/residue: 0.3536 time to fit residues: 210.4824 Evaluate side-chains 308 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 281 time to evaluate : 2.905 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2366 time to fit residues: 15.8890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 275 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN A 502 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN ** A 716 HIS ** 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 985 GLN A1005 ASN A1018 ASN ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN B 613 ASN ** 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 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN ** C 716 HIS ** 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** C 985 GLN C 999 GLN C1080 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 25374 Z= 0.443 Angle : 0.819 11.288 34569 Z= 0.438 Chirality : 0.050 0.206 3906 Planarity : 0.006 0.064 4512 Dihedral : 6.473 38.305 3486 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 3.01 % Allowed : 12.27 % Favored : 84.71 % 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: -0.82 (0.15), residues: 3189 helix: 1.05 (0.18), residues: 876 sheet: -0.13 (0.20), residues: 567 loop : -1.59 (0.15), residues: 1746 *********************** 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 407 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 324 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 49 residues processed: 388 average time/residue: 0.3454 time to fit residues: 217.2587 Evaluate side-chains 328 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 279 time to evaluate : 2.732 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.2673 time to fit residues: 27.0404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.0470 chunk 276 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 307 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 696 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** B 572 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 572 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** C 999 GLN C1018 ASN C1080 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: 0.7495 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25374 Z= 0.215 Angle : 0.649 9.226 34569 Z= 0.351 Chirality : 0.045 0.200 3906 Planarity : 0.005 0.056 4512 Dihedral : 6.029 37.329 3486 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 1.27 % Allowed : 14.67 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.51 (0.15), residues: 3189 helix: 1.44 (0.18), residues: 885 sheet: -0.13 (0.20), residues: 564 loop : -1.40 (0.15), residues: 1740 *********************** 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 373 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 338 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 18 residues processed: 358 average time/residue: 0.3564 time to fit residues: 206.8228 Evaluate side-chains 304 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 286 time to evaluate : 2.800 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2371 time to fit residues: 11.6582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 chunk 174 optimal weight: 0.6980 chunk 259 optimal weight: 0.9980 chunk 171 optimal weight: 0.5980 chunk 306 optimal weight: 6.9990 chunk 191 optimal weight: 0.0980 chunk 186 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN A 407 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** B1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25374 Z= 0.213 Angle : 0.635 10.116 34569 Z= 0.344 Chirality : 0.045 0.261 3906 Planarity : 0.005 0.053 4512 Dihedral : 5.886 35.774 3486 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.23 % Allowed : 15.25 % Favored : 83.51 % 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: -0.44 (0.15), residues: 3189 helix: 1.50 (0.18), residues: 891 sheet: -0.16 (0.20), residues: 597 loop : -1.37 (0.15), residues: 1701 *********************** 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 338 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 304 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 16 residues processed: 328 average time/residue: 0.3588 time to fit residues: 190.7275 Evaluate side-chains 287 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 271 time to evaluate : 2.873 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2291 time to fit residues: 10.8919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN B 314 GLN ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 613 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 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** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 ASN ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25374 Z= 0.336 Angle : 0.713 12.150 34569 Z= 0.382 Chirality : 0.047 0.205 3906 Planarity : 0.005 0.057 4512 Dihedral : 6.108 35.259 3486 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.16 % Allowed : 15.87 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.65 (0.15), residues: 3189 helix: 1.28 (0.18), residues: 885 sheet: -0.24 (0.20), residues: 600 loop : -1.48 (0.15), residues: 1704 *********************** 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 329 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 297 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 317 average time/residue: 0.3491 time to fit residues: 180.5263 Evaluate side-chains 284 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 263 time to evaluate : 2.926 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2670 time to fit residues: 13.9751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 0.4980 chunk 293 optimal weight: 4.9990 chunk 267 optimal weight: 0.4980 chunk 285 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 284 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN ** B1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 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** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1097 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25374 Z= 0.220 Angle : 0.637 9.320 34569 Z= 0.344 Chirality : 0.044 0.192 3906 Planarity : 0.005 0.057 4512 Dihedral : 5.904 34.523 3486 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 0.62 % Allowed : 16.45 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: -0.51 (0.15), residues: 3189 helix: 1.46 (0.18), residues: 894 sheet: -0.26 (0.20), residues: 612 loop : -1.41 (0.15), residues: 1683 *********************** 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 323 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 306 time to evaluate : 2.821 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 outliers start: 17 outliers final: 10 residues processed: 316 average time/residue: 0.3534 time to fit residues: 180.6726 Evaluate side-chains 281 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 271 time to evaluate : 2.963 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2331 time to fit residues: 8.5465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 3.9990 chunk 302 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 194 optimal weight: 0.0980 chunk 154 optimal weight: 0.0770 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 ASN ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 ASN ** B 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 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** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25374 Z= 0.279 Angle : 0.678 9.713 34569 Z= 0.364 Chirality : 0.045 0.211 3906 Planarity : 0.005 0.063 4512 Dihedral : 5.975 34.371 3486 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.25 % Favored : 91.69 % Rotamer: Outliers : 0.47 % Allowed : 17.18 % Favored : 82.35 % 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: -0.71 (0.15), residues: 3189 helix: 1.20 (0.18), residues: 912 sheet: -0.27 (0.20), residues: 615 loop : -1.56 (0.15), residues: 1662 ********************** 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 301 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 288 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 294 average time/residue: 0.3586 time to fit residues: 170.8702 Evaluate side-chains 281 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 270 time to evaluate : 2.777 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2361 time to fit residues: 8.7069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.6980 chunk 268 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 252 optimal weight: 0.0020 chunk 105 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 GLN ** 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** ** C1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.185401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.177425 restraints weight = 40547.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.171071 restraints weight = 59271.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170793 restraints weight = 85242.728| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.6355 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= 0.206 Angle : 0.633 9.925 34569 Z= 0.340 Chirality : 0.044 0.180 3906 Planarity : 0.005 0.061 4512 Dihedral : 5.827 33.544 3486 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.60 % Rotamer: Outliers : 0.40 % Allowed : 17.36 % Favored : 82.24 % 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: -0.57 (0.15), residues: 3189 helix: 1.34 (0.18), residues: 918 sheet: -0.22 (0.20), residues: 615 loop : -1.48 (0.15), residues: 1656 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5072.02 seconds wall clock time: 93 minutes 18.63 seconds (5598.63 seconds total)