Starting phenix.real_space_refine on Thu Feb 22 00:46:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk7_16091/02_2024/8bk7_16091.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk7_16091/02_2024/8bk7_16091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk7_16091/02_2024/8bk7_16091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk7_16091/02_2024/8bk7_16091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk7_16091/02_2024/8bk7_16091.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bk7_16091/02_2024/8bk7_16091.pdb" } resolution = 3.3 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= 0.013 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 152 5.16 5 C 20552 2.51 5 N 5760 2.21 5 O 6036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ASP 234": "OD1" <-> "OD2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A ASP 280": "OD1" <-> "OD2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 369": "OE1" <-> "OE2" Residue "A ASP 375": "OD1" <-> "OD2" Residue "A TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 469": "OD1" <-> "OD2" Residue "A TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A ASP 579": "OD1" <-> "OD2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 594": "OD1" <-> "OD2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A ASP 671": "OD1" <-> "OD2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ASP 746": "OD1" <-> "OD2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A ASP 875": "OD1" <-> "OD2" Residue "A ASP 919": "OD1" <-> "OD2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A GLU 980": "OE1" <-> "OE2" Residue "A PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 130": "OD1" <-> "OD2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 172": "OD1" <-> "OD2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 233": "OD1" <-> "OD2" Residue "B ASP 234": "OD1" <-> "OD2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ASP 280": "OD1" <-> "OD2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B ASP 319": "OD1" <-> "OD2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 358": "OE1" <-> "OE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B GLU 369": "OE1" <-> "OE2" Residue "B ASP 375": "OD1" <-> "OD2" Residue "B TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 469": "OD1" <-> "OD2" Residue "B TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 509": "OD1" <-> "OD2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B ASP 579": "OD1" <-> "OD2" Residue "B GLU 580": "OE1" <-> "OE2" Residue "B TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 594": "OD1" <-> "OD2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 667": "OE1" <-> "OE2" Residue "B ASP 671": "OD1" <-> "OD2" Residue "B GLU 681": "OE1" <-> "OE2" Residue "B ASP 746": "OD1" <-> "OD2" Residue "B GLU 750": "OE1" <-> "OE2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 792": "OD1" <-> "OD2" Residue "B TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B GLU 871": "OE1" <-> "OE2" Residue "B ASP 875": "OD1" <-> "OD2" Residue "B ASP 919": "OD1" <-> "OD2" Residue "B PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "B GLU 969": "OE1" <-> "OE2" Residue "B GLU 980": "OE1" <-> "OE2" Residue "B PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 71": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 130": "OD1" <-> "OD2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C ASP 234": "OD1" <-> "OD2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C ASP 280": "OD1" <-> "OD2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ASP 319": "OD1" <-> "OD2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C GLU 369": "OE1" <-> "OE2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 469": "OD1" <-> "OD2" Residue "C TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 509": "OD1" <-> "OD2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C ASP 572": "OD1" <-> "OD2" Residue "C ASP 579": "OD1" <-> "OD2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 594": "OD1" <-> "OD2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C GLU 667": "OE1" <-> "OE2" Residue "C ASP 671": "OD1" <-> "OD2" Residue "C GLU 681": "OE1" <-> "OE2" Residue "C ASP 746": "OD1" <-> "OD2" Residue "C GLU 750": "OE1" <-> "OE2" Residue "C PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 792": "OD1" <-> "OD2" Residue "C TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 819": "OE1" <-> "OE2" Residue "C GLU 871": "OE1" <-> "OE2" Residue "C ASP 875": "OD1" <-> "OD2" Residue "C ASP 919": "OD1" <-> "OD2" Residue "C PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 943": "OE1" <-> "OE2" Residue "C GLU 969": "OE1" <-> "OE2" Residue "C GLU 980": "OE1" <-> "OE2" Residue "C PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 172": "OD1" <-> "OD2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D ASP 224": "OD1" <-> "OD2" Residue "D PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D ASP 234": "OD1" <-> "OD2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ASP 280": "OD1" <-> "OD2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ASP 319": "OD1" <-> "OD2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D GLU 369": "OE1" <-> "OE2" Residue "D ASP 375": "OD1" <-> "OD2" Residue "D TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 469": "OD1" <-> "OD2" Residue "D TYR 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 509": "OD1" <-> "OD2" Residue "D GLU 529": "OE1" <-> "OE2" Residue "D ASP 572": "OD1" <-> "OD2" Residue "D ASP 579": "OD1" <-> "OD2" Residue "D GLU 580": "OE1" <-> "OE2" Residue "D TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 594": "OD1" <-> "OD2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 619": "OE1" <-> "OE2" Residue "D PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D GLU 667": "OE1" <-> "OE2" Residue "D ASP 671": "OD1" <-> "OD2" Residue "D GLU 681": "OE1" <-> "OE2" Residue "D ASP 746": "OD1" <-> "OD2" Residue "D GLU 750": "OE1" <-> "OE2" Residue "D PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 792": "OD1" <-> "OD2" Residue "D TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 819": "OE1" <-> "OE2" Residue "D GLU 871": "OE1" <-> "OE2" Residue "D ASP 875": "OD1" <-> "OD2" Residue "D ASP 919": "OD1" <-> "OD2" Residue "D PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 943": "OE1" <-> "OE2" Residue "D GLU 969": "OE1" <-> "OE2" Residue "D GLU 980": "OE1" <-> "OE2" Residue "D PHE 989": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32500 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Chain: "B" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Chain: "C" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Chain: "D" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Time building chain proxies: 15.78, per 1000 atoms: 0.49 Number of scatterers: 32500 At special positions: 0 Unit cell: (194.666, 150.086, 105.506, 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 152 16.00 O 6036 8.00 N 5760 7.00 C 20552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.02 Conformation dependent library (CDL) restraints added in 5.7 seconds 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7520 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 52 sheets defined 16.9% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.687A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.608A pdb=" N GLY A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.862A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 4.030A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.758A pdb=" N ARG A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.670A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.653A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 614 through 623 removed outlier: 4.137A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.564A pdb=" N TYR A 926 " --> pdb=" O SER A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.641A pdb=" N GLN A1008 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.687A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.608A pdb=" N GLY B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.862A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 4.030A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.758A pdb=" N ARG B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.670A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.654A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 614 through 623 removed outlier: 4.137A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 923 through 926 removed outlier: 3.564A pdb=" N TYR B 926 " --> pdb=" O SER B 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.641A pdb=" N GLN B1008 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.687A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.608A pdb=" N GLY C 94 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.863A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 4.030A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.758A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.671A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.653A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 614 through 623 removed outlier: 4.138A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.564A pdb=" N TYR C 926 " --> pdb=" O SER C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.640A pdb=" N GLN C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.687A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.607A pdb=" N GLY D 94 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.862A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 4.030A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.758A pdb=" N ARG D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.670A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.653A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 614 through 623 removed outlier: 4.138A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 923 through 926 removed outlier: 3.564A pdb=" N TYR D 926 " --> pdb=" O SER D 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 removed outlier: 3.641A pdb=" N GLN D1008 " --> pdb=" O ALA D1005 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.781A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 129 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.679A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 230 removed outlier: 3.519A pdb=" N CYS A 247 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN A 245 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A 225 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 243 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 227 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU A 241 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 229 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 239 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.772A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU A 254 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 removed outlier: 7.994A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 386 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 356 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.168A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 664 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.085A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.837A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.459A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.683A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.542A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 833 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.837A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.782A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 129 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.679A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 230 removed outlier: 3.519A pdb=" N CYS B 247 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN B 245 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B 225 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU B 243 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL B 227 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU B 241 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 229 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 239 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.773A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU B 254 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC2, first strand: chain 'B' and resid 484 through 485 removed outlier: 7.995A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 386 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 356 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC4, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.168A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 664 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.085A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.837A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.900A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.459A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.683A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.542A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 833 " --> pdb=" O LEU B 830 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.837A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.900A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.781A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 129 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD2, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.679A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 230 removed outlier: 3.519A pdb=" N CYS C 247 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN C 245 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE C 225 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU C 243 " --> pdb=" O PHE C 225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL C 227 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU C 241 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR C 229 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 239 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.773A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU C 254 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD6, first strand: chain 'C' and resid 484 through 485 removed outlier: 7.995A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 386 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 356 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AD8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.168A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 664 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.085A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.836A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.460A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.683A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.542A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 833 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.836A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.781A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 129 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE6, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.679A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 221 through 230 removed outlier: 3.519A pdb=" N CYS D 247 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN D 245 " --> pdb=" O SER D 223 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE D 225 " --> pdb=" O GLU D 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU D 243 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL D 227 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU D 241 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR D 229 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D 239 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.772A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU D 254 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF1, first strand: chain 'D' and resid 484 through 485 removed outlier: 7.994A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA D 386 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 356 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF3, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF4, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.168A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 664 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.085A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.836A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.460A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.683A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.542A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 833 " --> pdb=" O LEU D 830 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.836A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) 1232 hydrogen bonds defined for protein. 3228 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: 17.08 Time building geometry restraints manager: 12.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10968 1.34 - 1.46: 7919 1.46 - 1.58: 14333 1.58 - 1.70: 8 1.70 - 1.82: 240 Bond restraints: 33468 Sorted by residual: bond pdb=" CB PRO C 596 " pdb=" CG PRO C 596 " ideal model delta sigma weight residual 1.506 1.617 -0.111 3.90e-02 6.57e+02 8.11e+00 bond pdb=" CB PRO B 596 " pdb=" CG PRO B 596 " ideal model delta sigma weight residual 1.506 1.616 -0.110 3.90e-02 6.57e+02 8.00e+00 bond pdb=" CB PRO D 596 " pdb=" CG PRO D 596 " ideal model delta sigma weight residual 1.506 1.616 -0.110 3.90e-02 6.57e+02 7.97e+00 bond pdb=" CB PRO A 596 " pdb=" CG PRO A 596 " ideal model delta sigma weight residual 1.506 1.616 -0.110 3.90e-02 6.57e+02 7.92e+00 bond pdb=" CB PRO A 32 " pdb=" CG PRO A 32 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.40e+00 ... (remaining 33463 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.28: 700 104.28 - 111.76: 15126 111.76 - 119.23: 11906 119.23 - 126.70: 16977 126.70 - 134.17: 951 Bond angle restraints: 45660 Sorted by residual: angle pdb=" CA PRO B 596 " pdb=" N PRO B 596 " pdb=" CD PRO B 596 " ideal model delta sigma weight residual 111.50 96.81 14.69 1.40e+00 5.10e-01 1.10e+02 angle pdb=" CA PRO A 596 " pdb=" N PRO A 596 " pdb=" CD PRO A 596 " ideal model delta sigma weight residual 111.50 96.87 14.63 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO D 596 " pdb=" N PRO D 596 " pdb=" CD PRO D 596 " ideal model delta sigma weight residual 111.50 96.87 14.63 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO C 596 " pdb=" N PRO C 596 " pdb=" CD PRO C 596 " ideal model delta sigma weight residual 111.50 96.90 14.60 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" CD PRO C 32 " ideal model delta sigma weight residual 112.00 100.97 11.03 1.40e+00 5.10e-01 6.21e+01 ... (remaining 45655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 16600 17.80 - 35.61: 2125 35.61 - 53.41: 683 53.41 - 71.21: 128 71.21 - 89.02: 60 Dihedral angle restraints: 19596 sinusoidal: 7912 harmonic: 11684 Sorted by residual: dihedral pdb=" CA ASP B 598 " pdb=" C ASP B 598 " pdb=" N ARG B 599 " pdb=" CA ARG B 599 " ideal model delta harmonic sigma weight residual -180.00 -148.93 -31.07 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASP A 598 " pdb=" C ASP A 598 " pdb=" N ARG A 599 " pdb=" CA ARG A 599 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA ASP C 598 " pdb=" C ASP C 598 " pdb=" N ARG C 599 " pdb=" CA ARG C 599 " ideal model delta harmonic sigma weight residual -180.00 -148.97 -31.03 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 19593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3979 0.059 - 0.119: 671 0.119 - 0.178: 88 0.178 - 0.237: 6 0.237 - 0.296: 8 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" C PRO A 32 " pdb=" CB PRO A 32 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" C PRO C 32 " pdb=" CB PRO C 32 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4749 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 682 " -0.099 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO B 683 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 683 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 683 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 682 " 0.099 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO C 683 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO C 683 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO C 683 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 682 " 0.099 5.00e-02 4.00e+02 1.46e-01 3.40e+01 pdb=" N PRO A 683 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO A 683 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 683 " 0.075 5.00e-02 4.00e+02 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1284 2.71 - 3.26: 29293 3.26 - 3.81: 56401 3.81 - 4.35: 70145 4.35 - 4.90: 121069 Nonbonded interactions: 278192 Sorted by model distance: nonbonded pdb=" OE2 GLU B 724 " pdb=" OG SER C 874 " model vdw 2.168 2.440 nonbonded pdb=" OE2 GLU A 724 " pdb=" OG SER D 874 " model vdw 2.168 2.440 nonbonded pdb=" OG SER B 874 " pdb=" OE2 GLU C 724 " model vdw 2.168 2.440 nonbonded pdb=" OG SER A 874 " pdb=" OE2 GLU D 724 " model vdw 2.168 2.440 nonbonded pdb=" OD2 ASP C 234 " pdb=" OG SER C 236 " model vdw 2.250 2.440 ... (remaining 278187 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' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 3.240 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 86.590 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 33468 Z= 0.283 Angle : 0.775 14.687 45660 Z= 0.420 Chirality : 0.047 0.296 4752 Planarity : 0.008 0.146 6036 Dihedral : 18.141 89.017 12076 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.95 % Allowed : 27.03 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.64 (0.13), residues: 4036 helix: -1.03 (0.22), residues: 444 sheet: 0.45 (0.14), residues: 1420 loop : -0.86 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B 654 HIS 0.013 0.001 HIS A 395 PHE 0.019 0.002 PHE C 231 TYR 0.034 0.002 TYR C 100 ARG 0.013 0.001 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 605 time to evaluate : 3.560 Fit side-chains REVERT: A 249 GLU cc_start: 0.5290 (mm-30) cc_final: 0.4867 (tm-30) REVERT: A 277 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: A 334 GLU cc_start: 0.8134 (pp20) cc_final: 0.7808 (pt0) REVERT: A 395 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.6416 (t-90) REVERT: A 424 ASN cc_start: 0.8393 (p0) cc_final: 0.7952 (p0) REVERT: A 502 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: A 781 ARG cc_start: 0.8156 (ptm160) cc_final: 0.7417 (ptp90) REVERT: A 835 LEU cc_start: 0.8138 (tm) cc_final: 0.7923 (tp) REVERT: A 970 THR cc_start: 0.7702 (m) cc_final: 0.7129 (p) REVERT: A 1022 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6370 (tm-30) REVERT: B 249 GLU cc_start: 0.5258 (mm-30) cc_final: 0.4828 (tm-30) REVERT: B 277 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6482 (mm-30) REVERT: B 334 GLU cc_start: 0.8092 (pp20) cc_final: 0.7762 (pt0) REVERT: B 395 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6376 (t-90) REVERT: B 424 ASN cc_start: 0.8386 (p0) cc_final: 0.7948 (p0) REVERT: B 487 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: B 502 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7884 (mpp) REVERT: B 781 ARG cc_start: 0.8177 (ptm160) cc_final: 0.7406 (ptp90) REVERT: B 835 LEU cc_start: 0.8162 (tm) cc_final: 0.7951 (tp) REVERT: B 970 THR cc_start: 0.7712 (m) cc_final: 0.7138 (p) REVERT: B 1022 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6382 (tm-30) REVERT: C 33 PHE cc_start: 0.7931 (m-80) cc_final: 0.7702 (m-10) REVERT: C 249 GLU cc_start: 0.5282 (mm-30) cc_final: 0.4847 (tm-30) REVERT: C 277 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6473 (mm-30) REVERT: C 334 GLU cc_start: 0.8082 (pp20) cc_final: 0.7762 (pt0) REVERT: C 395 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.6338 (t-90) REVERT: C 424 ASN cc_start: 0.8390 (p0) cc_final: 0.7966 (p0) REVERT: C 502 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7873 (mpp) REVERT: C 781 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7406 (ptp90) REVERT: C 835 LEU cc_start: 0.8199 (tm) cc_final: 0.7979 (tp) REVERT: C 970 THR cc_start: 0.7702 (m) cc_final: 0.7109 (p) REVERT: C 1022 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6341 (tm-30) REVERT: D 249 GLU cc_start: 0.5315 (mm-30) cc_final: 0.4890 (tm-30) REVERT: D 277 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6192 (mm-30) REVERT: D 334 GLU cc_start: 0.8131 (pp20) cc_final: 0.7808 (pt0) REVERT: D 388 ARG cc_start: 0.8640 (ttt180) cc_final: 0.8340 (ttt180) REVERT: D 395 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.6376 (t-90) REVERT: D 424 ASN cc_start: 0.8400 (p0) cc_final: 0.7970 (p0) REVERT: D 476 LYS cc_start: 0.8257 (tptp) cc_final: 0.8052 (mmmt) REVERT: D 487 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6816 (tm-30) REVERT: D 502 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7862 (mpp) REVERT: D 781 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7386 (ptp90) REVERT: D 835 LEU cc_start: 0.8158 (tm) cc_final: 0.7941 (tp) REVERT: D 970 THR cc_start: 0.7698 (m) cc_final: 0.7109 (p) REVERT: D 1022 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6321 (tm-30) outliers start: 102 outliers final: 68 residues processed: 677 average time/residue: 0.4572 time to fit residues: 492.7370 Evaluate side-chains 639 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 558 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 525 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 1002 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 4.9990 chunk 306 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN A 634 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 147 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN B 634 GLN B 653 HIS B 990 HIS C 147 ASN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN C 634 GLN C 653 HIS ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS D 147 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN D 634 GLN ** D 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 33468 Z= 0.374 Angle : 0.636 8.559 45660 Z= 0.335 Chirality : 0.047 0.182 4752 Planarity : 0.006 0.093 6036 Dihedral : 7.192 48.999 4571 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 6.39 % Allowed : 22.42 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.13), residues: 4036 helix: -0.60 (0.22), residues: 488 sheet: 0.78 (0.14), residues: 1376 loop : -0.68 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 553 HIS 0.008 0.002 HIS C1015 PHE 0.019 0.002 PHE D 384 TYR 0.020 0.002 TYR B 100 ARG 0.007 0.001 ARG C 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 660 time to evaluate : 3.708 Fit side-chains REVERT: A 177 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 202 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8227 (pmm) REVERT: A 249 GLU cc_start: 0.5380 (mm-30) cc_final: 0.5049 (tm-30) REVERT: A 250 LEU cc_start: 0.6627 (tp) cc_final: 0.6160 (tp) REVERT: A 264 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8396 (pm20) REVERT: A 334 GLU cc_start: 0.8227 (pp20) cc_final: 0.7947 (pt0) REVERT: A 388 ARG cc_start: 0.8726 (ttt180) cc_final: 0.8511 (ttt180) REVERT: A 395 HIS cc_start: 0.7316 (OUTLIER) cc_final: 0.5938 (t70) REVERT: A 781 ARG cc_start: 0.8092 (ptm160) cc_final: 0.7282 (ptp90) REVERT: A 952 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7957 (ttp-170) REVERT: A 965 GLN cc_start: 0.6737 (tp40) cc_final: 0.6410 (tp40) REVERT: A 969 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7792 (mp0) REVERT: A 980 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6407 (mm-30) REVERT: A 1022 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6660 (tm-30) REVERT: B 67 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8024 (mm-30) REVERT: B 177 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8199 (tp) REVERT: B 202 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8227 (pmm) REVERT: B 249 GLU cc_start: 0.5354 (mm-30) cc_final: 0.5020 (tm-30) REVERT: B 250 LEU cc_start: 0.6578 (tp) cc_final: 0.6094 (tp) REVERT: B 264 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: B 388 ARG cc_start: 0.8727 (ttt180) cc_final: 0.8517 (ttt180) REVERT: B 395 HIS cc_start: 0.7524 (OUTLIER) cc_final: 0.6256 (t70) REVERT: B 781 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7279 (ptp90) REVERT: B 852 SER cc_start: 0.9049 (p) cc_final: 0.8849 (p) REVERT: B 952 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8027 (ttp-170) REVERT: B 969 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: B 980 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6434 (mm-30) REVERT: B 1022 GLN cc_start: 0.7140 (mm-40) cc_final: 0.6668 (tm-30) REVERT: C 67 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 177 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8204 (tp) REVERT: C 202 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8196 (pmm) REVERT: C 249 GLU cc_start: 0.5377 (mm-30) cc_final: 0.5044 (tm-30) REVERT: C 250 LEU cc_start: 0.6608 (tp) cc_final: 0.6119 (tp) REVERT: C 264 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8376 (pm20) REVERT: C 395 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.5919 (t70) REVERT: C 781 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7282 (ptp90) REVERT: C 852 SER cc_start: 0.9051 (p) cc_final: 0.8849 (p) REVERT: C 965 GLN cc_start: 0.6749 (tp40) cc_final: 0.6369 (tp40) REVERT: C 969 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: C 980 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6443 (mm-30) REVERT: C 1022 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6638 (tm-30) REVERT: D 67 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8065 (mm-30) REVERT: D 135 GLN cc_start: 0.6689 (mm110) cc_final: 0.6454 (mt0) REVERT: D 177 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8215 (tp) REVERT: D 202 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8191 (pmm) REVERT: D 249 GLU cc_start: 0.5382 (mm-30) cc_final: 0.5050 (tm-30) REVERT: D 250 LEU cc_start: 0.6627 (tp) cc_final: 0.6153 (tp) REVERT: D 334 GLU cc_start: 0.8221 (pp20) cc_final: 0.7951 (pt0) REVERT: D 388 ARG cc_start: 0.8718 (ttt180) cc_final: 0.8504 (ttt180) REVERT: D 395 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.5695 (t70) REVERT: D 423 MET cc_start: 0.8311 (tpp) cc_final: 0.8017 (ttm) REVERT: D 781 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7259 (ptp90) REVERT: D 925 MET cc_start: 0.9138 (mmm) cc_final: 0.8885 (mmm) REVERT: D 965 GLN cc_start: 0.6729 (tp40) cc_final: 0.6368 (tp40) REVERT: D 969 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: D 980 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6449 (mm-30) REVERT: D 1022 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6628 (tm-30) outliers start: 221 outliers final: 127 residues processed: 790 average time/residue: 0.4748 time to fit residues: 589.9106 Evaluate side-chains 766 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 618 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 952 ARG Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 525 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 991 MET Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 991 MET Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 367 optimal weight: 20.0000 chunk 397 optimal weight: 9.9990 chunk 327 optimal weight: 2.9990 chunk 364 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 294 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 623 GLN A 634 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN B 634 GLN C 370 GLN C 634 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 634 GLN ** D 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 33468 Z= 0.408 Angle : 0.634 7.053 45660 Z= 0.335 Chirality : 0.048 0.174 4752 Planarity : 0.006 0.076 6036 Dihedral : 6.121 56.339 4472 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 7.99 % Allowed : 20.43 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.37 (0.13), residues: 4036 helix: -0.57 (0.22), residues: 488 sheet: 0.70 (0.14), residues: 1396 loop : -0.78 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 553 HIS 0.007 0.002 HIS D 151 PHE 0.014 0.002 PHE B 384 TYR 0.017 0.002 TYR A1016 ARG 0.006 0.001 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 682 time to evaluate : 3.954 Fit side-chains REVERT: A 131 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7242 (mm-30) REVERT: A 177 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8037 (tp) REVERT: A 202 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7988 (pmm) REVERT: A 243 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 395 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.6067 (t70) REVERT: A 423 MET cc_start: 0.8356 (ttm) cc_final: 0.7709 (ttm) REVERT: A 502 MET cc_start: 0.8507 (mtp) cc_final: 0.8224 (mtt) REVERT: A 781 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7241 (ptp90) REVERT: A 952 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7912 (ttp-170) REVERT: A 965 GLN cc_start: 0.6842 (tp40) cc_final: 0.6373 (tp40) REVERT: A 969 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 1022 GLN cc_start: 0.7273 (mm-40) cc_final: 0.6440 (tm-30) REVERT: B 177 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8119 (tp) REVERT: B 202 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8067 (pmm) REVERT: B 243 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7981 (mm-30) REVERT: B 395 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.6046 (t70) REVERT: B 423 MET cc_start: 0.8356 (ttm) cc_final: 0.7715 (ttm) REVERT: B 502 MET cc_start: 0.8505 (mtp) cc_final: 0.8153 (mtm) REVERT: B 781 ARG cc_start: 0.8068 (ptm160) cc_final: 0.7241 (ptp90) REVERT: B 952 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8073 (ttp-170) REVERT: B 969 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: B 1022 GLN cc_start: 0.7287 (mm-40) cc_final: 0.6454 (tm-30) REVERT: C 177 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8214 (tp) REVERT: C 202 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.7994 (pmm) REVERT: C 243 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8034 (mm-30) REVERT: C 395 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6057 (t70) REVERT: C 423 MET cc_start: 0.8357 (ttm) cc_final: 0.7705 (ttm) REVERT: C 502 MET cc_start: 0.8527 (mtp) cc_final: 0.8200 (mtm) REVERT: C 781 ARG cc_start: 0.8077 (ptm160) cc_final: 0.7197 (ptp90) REVERT: C 832 ASP cc_start: 0.5049 (t0) cc_final: 0.4803 (t0) REVERT: C 952 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8045 (ttp-170) REVERT: C 965 GLN cc_start: 0.6826 (tp40) cc_final: 0.6381 (tp40) REVERT: C 969 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: C 1022 GLN cc_start: 0.7282 (mm-40) cc_final: 0.6442 (tm-30) REVERT: D 177 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8139 (tp) REVERT: D 202 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7966 (pmm) REVERT: D 243 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7988 (mm-30) REVERT: D 395 HIS cc_start: 0.7527 (OUTLIER) cc_final: 0.6038 (t70) REVERT: D 423 MET cc_start: 0.8351 (tpp) cc_final: 0.8085 (ttm) REVERT: D 502 MET cc_start: 0.8551 (mtp) cc_final: 0.8153 (mtm) REVERT: D 781 ARG cc_start: 0.8095 (ptm160) cc_final: 0.7226 (ptp90) REVERT: D 832 ASP cc_start: 0.5050 (t0) cc_final: 0.4815 (t0) REVERT: D 965 GLN cc_start: 0.6813 (tp40) cc_final: 0.6393 (tp40) REVERT: D 969 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: D 1022 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6433 (tm-30) outliers start: 276 outliers final: 183 residues processed: 853 average time/residue: 0.4446 time to fit residues: 599.9444 Evaluate side-chains 841 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 639 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 594 ASP Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 952 ARG Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 594 ASP Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 952 ARG Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 991 MET Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 991 MET Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 0.0000 chunk 276 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 175 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 368 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 192 optimal weight: 1.9990 chunk 349 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 147 ASN A 370 GLN A 573 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 623 GLN C 102 ASN C 147 ASN C 370 GLN C 965 GLN D 102 ASN D 147 ASN D 370 GLN D 573 GLN ** D 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 33468 Z= 0.246 Angle : 0.549 6.324 45660 Z= 0.287 Chirality : 0.045 0.173 4752 Planarity : 0.005 0.066 6036 Dihedral : 5.587 46.744 4468 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 6.54 % Allowed : 22.16 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.25 (0.13), residues: 4036 helix: -0.29 (0.23), residues: 488 sheet: 0.79 (0.14), residues: 1352 loop : -0.73 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 553 HIS 0.005 0.001 HIS D 151 PHE 0.010 0.001 PHE B 384 TYR 0.015 0.002 TYR C 588 ARG 0.005 0.001 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 697 time to evaluate : 3.753 Fit side-chains REVERT: A 131 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 135 GLN cc_start: 0.7127 (mt0) cc_final: 0.6831 (mt0) REVERT: A 177 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8113 (tp) REVERT: A 202 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8124 (pmm) REVERT: A 243 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8125 (mm-30) REVERT: A 288 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7611 (ttm170) REVERT: A 502 MET cc_start: 0.8451 (mtp) cc_final: 0.8048 (mtm) REVERT: A 781 ARG cc_start: 0.7912 (ptm160) cc_final: 0.7113 (ptp90) REVERT: A 964 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7208 (tp40) REVERT: A 965 GLN cc_start: 0.6762 (tp40) cc_final: 0.6307 (tp40) REVERT: A 969 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: A 1022 GLN cc_start: 0.7381 (mm-40) cc_final: 0.6527 (tm-30) REVERT: B 177 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8103 (tp) REVERT: B 202 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8107 (pmm) REVERT: B 243 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8121 (mm-30) REVERT: B 288 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7481 (ttm170) REVERT: B 487 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 502 MET cc_start: 0.8477 (mtp) cc_final: 0.8053 (mtm) REVERT: B 781 ARG cc_start: 0.7974 (ptm160) cc_final: 0.7123 (ptp90) REVERT: B 969 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 1022 GLN cc_start: 0.7387 (mm-40) cc_final: 0.6527 (tm-30) REVERT: C 177 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8101 (tp) REVERT: C 202 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8123 (pmm) REVERT: C 243 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8007 (mm-30) REVERT: C 487 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7196 (tm-30) REVERT: C 502 MET cc_start: 0.8465 (mtp) cc_final: 0.8063 (mtm) REVERT: C 781 ARG cc_start: 0.7986 (ptm160) cc_final: 0.7129 (ptp90) REVERT: C 964 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7200 (tp40) REVERT: C 965 GLN cc_start: 0.6892 (tp-100) cc_final: 0.6426 (tp40) REVERT: C 969 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7730 (mp0) REVERT: C 1022 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6486 (tm-30) REVERT: D 177 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8097 (tp) REVERT: D 202 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8099 (pmm) REVERT: D 243 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8126 (mm-30) REVERT: D 288 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7609 (ttm170) REVERT: D 423 MET cc_start: 0.8333 (tpp) cc_final: 0.7946 (ttm) REVERT: D 502 MET cc_start: 0.8448 (mtp) cc_final: 0.8050 (mtm) REVERT: D 781 ARG cc_start: 0.7857 (ptm160) cc_final: 0.7078 (ptp90) REVERT: D 829 THR cc_start: 0.7446 (t) cc_final: 0.7071 (m) REVERT: D 952 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8110 (ttp-170) REVERT: D 965 GLN cc_start: 0.6750 (tp40) cc_final: 0.6295 (tp40) REVERT: D 969 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: D 1022 GLN cc_start: 0.7361 (mm-40) cc_final: 0.6483 (tm-30) outliers start: 226 outliers final: 130 residues processed: 857 average time/residue: 0.4907 time to fit residues: 666.0109 Evaluate side-chains 793 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 648 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 964 GLN Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 952 ARG Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 985 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 161 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 269 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 chunk 350 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 226 HIS A 370 GLN A 395 HIS A 719 GLN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 226 HIS B 370 GLN B 395 HIS B 623 GLN B 719 GLN C 147 ASN C 226 HIS C 370 GLN C 395 HIS C 719 GLN D 147 ASN D 226 HIS D 370 GLN D 395 HIS D 719 GLN ** D 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 33468 Z= 0.451 Angle : 0.650 8.209 45660 Z= 0.341 Chirality : 0.048 0.174 4752 Planarity : 0.005 0.065 6036 Dihedral : 5.910 51.216 4460 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 8.19 % Allowed : 19.65 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.13), residues: 4036 helix: -0.60 (0.23), residues: 488 sheet: 0.57 (0.13), residues: 1384 loop : -0.86 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 553 HIS 0.007 0.002 HIS B 151 PHE 0.012 0.002 PHE B 150 TYR 0.033 0.003 TYR B 100 ARG 0.006 0.001 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 676 time to evaluate : 3.734 Fit side-chains REVERT: A 131 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7465 (mm-30) REVERT: A 177 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8140 (tp) REVERT: A 202 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8021 (pmm) REVERT: A 243 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8483 (mm-30) REVERT: A 502 MET cc_start: 0.8697 (mtp) cc_final: 0.8308 (mtt) REVERT: A 654 TRP cc_start: 0.7449 (p90) cc_final: 0.7197 (p90) REVERT: A 781 ARG cc_start: 0.8015 (ptm160) cc_final: 0.7186 (ptp90) REVERT: A 791 ASN cc_start: 0.7585 (m-40) cc_final: 0.6974 (m-40) REVERT: A 952 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8041 (ttp-170) REVERT: A 965 GLN cc_start: 0.6788 (tp40) cc_final: 0.6373 (tp40) REVERT: A 969 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 1022 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6494 (tm-30) REVERT: B 177 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8152 (tp) REVERT: B 202 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8048 (pmm) REVERT: B 502 MET cc_start: 0.8568 (mtp) cc_final: 0.8217 (mtt) REVERT: B 654 TRP cc_start: 0.7381 (p90) cc_final: 0.7136 (p90) REVERT: B 781 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7182 (ptp90) REVERT: B 791 ASN cc_start: 0.7568 (m-40) cc_final: 0.6964 (m-40) REVERT: B 952 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8035 (ttp-170) REVERT: B 969 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: B 1022 GLN cc_start: 0.7472 (mm-40) cc_final: 0.6492 (tm-30) REVERT: C 202 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8051 (pmm) REVERT: C 502 MET cc_start: 0.8569 (mtp) cc_final: 0.8237 (mtt) REVERT: C 654 TRP cc_start: 0.7375 (p90) cc_final: 0.7139 (p90) REVERT: C 740 LEU cc_start: 0.8221 (tp) cc_final: 0.8017 (tp) REVERT: C 781 ARG cc_start: 0.8024 (ptm160) cc_final: 0.7185 (ptp90) REVERT: C 791 ASN cc_start: 0.7581 (m-40) cc_final: 0.6972 (m-40) REVERT: C 829 THR cc_start: 0.7512 (t) cc_final: 0.7126 (m) REVERT: C 832 ASP cc_start: 0.5348 (t0) cc_final: 0.5079 (t0) REVERT: C 952 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7981 (ttp-170) REVERT: C 969 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: C 1022 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6511 (tm-30) REVERT: D 177 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8228 (tp) REVERT: D 202 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8177 (pmm) REVERT: D 243 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8479 (mm-30) REVERT: D 502 MET cc_start: 0.8565 (mtp) cc_final: 0.8212 (mtt) REVERT: D 654 TRP cc_start: 0.7455 (p90) cc_final: 0.7206 (p90) REVERT: D 740 LEU cc_start: 0.8231 (tp) cc_final: 0.8022 (tp) REVERT: D 781 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7146 (ptp90) REVERT: D 791 ASN cc_start: 0.7579 (m-40) cc_final: 0.6969 (m-40) REVERT: D 829 THR cc_start: 0.7531 (t) cc_final: 0.7082 (m) REVERT: D 832 ASP cc_start: 0.5345 (t0) cc_final: 0.5075 (t0) REVERT: D 952 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7888 (ttp-170) REVERT: D 965 GLN cc_start: 0.6755 (tp40) cc_final: 0.6347 (tp40) REVERT: D 969 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: D 1022 GLN cc_start: 0.7421 (mm-40) cc_final: 0.6510 (tm-30) outliers start: 283 outliers final: 220 residues processed: 874 average time/residue: 0.4618 time to fit residues: 638.6025 Evaluate side-chains 889 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 654 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 797 GLU Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 952 ARG Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 797 GLU Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 952 ARG Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 991 MET Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 952 ARG Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 991 MET Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 390 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 205 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 226 HIS A 370 GLN A 395 HIS A 414 ASN ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 370 GLN B 395 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN C 147 ASN C 370 GLN C 395 HIS C 414 ASN C 573 GLN C 623 GLN D 147 ASN D 226 HIS D 370 GLN D 395 HIS D 414 ASN D 623 GLN ** D 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 33468 Z= 0.364 Angle : 0.609 9.123 45660 Z= 0.318 Chirality : 0.047 0.177 4752 Planarity : 0.005 0.061 6036 Dihedral : 5.812 49.144 4460 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 7.32 % Allowed : 21.24 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 4036 helix: -0.57 (0.23), residues: 488 sheet: 0.55 (0.13), residues: 1372 loop : -0.86 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 553 HIS 0.006 0.001 HIS D 151 PHE 0.013 0.002 PHE D 225 TYR 0.024 0.002 TYR C 100 ARG 0.009 0.001 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 698 time to evaluate : 3.984 Fit side-chains REVERT: A 46 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6761 (mtt90) REVERT: A 135 GLN cc_start: 0.7363 (mt0) cc_final: 0.6936 (mt0) REVERT: A 202 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8071 (pmm) REVERT: A 237 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.8047 (ttm-80) REVERT: A 502 MET cc_start: 0.8670 (mtp) cc_final: 0.8290 (mtt) REVERT: A 654 TRP cc_start: 0.7431 (p90) cc_final: 0.7204 (p90) REVERT: A 753 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6793 (p0) REVERT: A 781 ARG cc_start: 0.8000 (ptm160) cc_final: 0.7158 (ptp90) REVERT: A 791 ASN cc_start: 0.7584 (m-40) cc_final: 0.7132 (m110) REVERT: A 952 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8006 (ttp-170) REVERT: A 965 GLN cc_start: 0.6755 (tp40) cc_final: 0.6334 (tp40) REVERT: A 969 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: A 1022 GLN cc_start: 0.7466 (mm-40) cc_final: 0.6501 (tm-30) REVERT: B 46 ARG cc_start: 0.6988 (mtt90) cc_final: 0.6761 (mtt90) REVERT: B 202 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8105 (pmm) REVERT: B 237 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.8050 (ttm-80) REVERT: B 502 MET cc_start: 0.8684 (mtp) cc_final: 0.8282 (mtt) REVERT: B 654 TRP cc_start: 0.7368 (p90) cc_final: 0.7142 (p90) REVERT: B 753 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6789 (p0) REVERT: B 781 ARG cc_start: 0.7999 (ptm160) cc_final: 0.7156 (ptp90) REVERT: B 791 ASN cc_start: 0.7571 (m-40) cc_final: 0.7124 (m110) REVERT: B 952 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7995 (ttp-170) REVERT: B 969 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 1022 GLN cc_start: 0.7412 (mm-40) cc_final: 0.6515 (tm-30) REVERT: C 46 ARG cc_start: 0.6991 (mtt90) cc_final: 0.6760 (mtt90) REVERT: C 202 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8071 (pmm) REVERT: C 237 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.8045 (ttm-80) REVERT: C 502 MET cc_start: 0.8550 (mtp) cc_final: 0.8226 (mtt) REVERT: C 654 TRP cc_start: 0.7362 (p90) cc_final: 0.7139 (p90) REVERT: C 740 LEU cc_start: 0.8215 (tp) cc_final: 0.8011 (tp) REVERT: C 753 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.6916 (p0) REVERT: C 781 ARG cc_start: 0.8009 (ptm160) cc_final: 0.7160 (ptp90) REVERT: C 791 ASN cc_start: 0.7583 (m-40) cc_final: 0.7131 (m110) REVERT: C 829 THR cc_start: 0.7704 (t) cc_final: 0.7270 (m) REVERT: C 952 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7969 (ttp-170) REVERT: C 969 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: C 1022 GLN cc_start: 0.7414 (mm-40) cc_final: 0.6520 (tm-30) REVERT: D 46 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6759 (mtt90) REVERT: D 202 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8110 (pmm) REVERT: D 423 MET cc_start: 0.8478 (ttm) cc_final: 0.7771 (ttm) REVERT: D 502 MET cc_start: 0.8672 (mtp) cc_final: 0.8281 (mtt) REVERT: D 654 TRP cc_start: 0.7439 (p90) cc_final: 0.7216 (p90) REVERT: D 687 GLN cc_start: 0.7041 (mp10) cc_final: 0.6603 (mp10) REVERT: D 740 LEU cc_start: 0.8242 (tp) cc_final: 0.8041 (tp) REVERT: D 781 ARG cc_start: 0.7935 (ptm160) cc_final: 0.7116 (ptp90) REVERT: D 791 ASN cc_start: 0.7577 (m-40) cc_final: 0.6958 (m-40) REVERT: D 829 THR cc_start: 0.7790 (t) cc_final: 0.7192 (m) REVERT: D 952 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7836 (ttp-170) REVERT: D 965 GLN cc_start: 0.6885 (tp40) cc_final: 0.6405 (tp40) REVERT: D 969 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: D 1022 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6515 (tm-30) outliers start: 253 outliers final: 198 residues processed: 869 average time/residue: 0.4691 time to fit residues: 646.6707 Evaluate side-chains 904 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 691 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 797 GLU Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 952 ARG Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 648 ASP Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 952 ARG Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 379 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 952 ARG Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 285 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 329 optimal weight: 2.9990 chunk 218 optimal weight: 10.0000 chunk 389 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 370 GLN A 395 HIS ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 370 GLN B 395 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN C 370 GLN C 395 HIS C 573 GLN C 623 GLN ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN D 370 GLN D 395 HIS ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33468 Z= 0.180 Angle : 0.532 8.649 45660 Z= 0.276 Chirality : 0.044 0.179 4752 Planarity : 0.004 0.056 6036 Dihedral : 5.364 45.047 4460 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.98 % Allowed : 23.84 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: -0.26 (0.13), residues: 4036 helix: -0.20 (0.24), residues: 488 sheet: 0.71 (0.14), residues: 1352 loop : -0.71 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 553 HIS 0.006 0.001 HIS C 395 PHE 0.012 0.001 PHE D 225 TYR 0.028 0.002 TYR C 100 ARG 0.006 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 713 time to evaluate : 3.494 Fit side-chains REVERT: A 131 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7583 (mm-30) REVERT: A 135 GLN cc_start: 0.7326 (mt0) cc_final: 0.6849 (mt0) REVERT: A 202 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8033 (pmm) REVERT: A 237 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.8046 (ttm-80) REVERT: A 264 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: A 388 ARG cc_start: 0.8683 (ttt180) cc_final: 0.8424 (ttt180) REVERT: A 438 GLU cc_start: 0.8045 (pp20) cc_final: 0.7627 (pp20) REVERT: A 502 MET cc_start: 0.8581 (mtp) cc_final: 0.8176 (mtm) REVERT: A 753 ASN cc_start: 0.7147 (OUTLIER) cc_final: 0.6716 (p0) REVERT: A 781 ARG cc_start: 0.7950 (ptm160) cc_final: 0.7119 (ptp90) REVERT: A 791 ASN cc_start: 0.7571 (m-40) cc_final: 0.7003 (m-40) REVERT: A 965 GLN cc_start: 0.6867 (tp40) cc_final: 0.6397 (tp40) REVERT: A 969 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 1022 GLN cc_start: 0.7354 (mm-40) cc_final: 0.6510 (tm-30) REVERT: B 202 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8019 (pmm) REVERT: B 237 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.8042 (ttm-80) REVERT: B 264 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: B 388 ARG cc_start: 0.8677 (ttt180) cc_final: 0.8422 (ttt180) REVERT: B 438 GLU cc_start: 0.8046 (pp20) cc_final: 0.7635 (pp20) REVERT: B 502 MET cc_start: 0.8637 (mtp) cc_final: 0.8236 (mtm) REVERT: B 753 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6559 (p0) REVERT: B 781 ARG cc_start: 0.7946 (ptm160) cc_final: 0.7112 (ptp90) REVERT: B 791 ASN cc_start: 0.7558 (m-40) cc_final: 0.6991 (m-40) REVERT: B 969 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: B 1022 GLN cc_start: 0.7356 (mm-40) cc_final: 0.6506 (tm-30) REVERT: C 202 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8038 (pmm) REVERT: C 237 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.8043 (ttm-80) REVERT: C 264 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7550 (pm20) REVERT: C 438 GLU cc_start: 0.8047 (pp20) cc_final: 0.7627 (pp20) REVERT: C 502 MET cc_start: 0.8483 (mtp) cc_final: 0.8085 (mtm) REVERT: C 740 LEU cc_start: 0.8161 (tp) cc_final: 0.7955 (tp) REVERT: C 753 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6726 (p0) REVERT: C 781 ARG cc_start: 0.7961 (ptm160) cc_final: 0.7119 (ptp90) REVERT: C 791 ASN cc_start: 0.7573 (m-40) cc_final: 0.6987 (m-40) REVERT: C 829 THR cc_start: 0.7640 (t) cc_final: 0.7230 (m) REVERT: C 969 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: C 1022 GLN cc_start: 0.7358 (mm-40) cc_final: 0.6508 (tm-30) REVERT: D 202 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8076 (pmm) REVERT: D 237 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.8031 (ttm-80) REVERT: D 264 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: D 423 MET cc_start: 0.8188 (ttm) cc_final: 0.7624 (ttm) REVERT: D 438 GLU cc_start: 0.8042 (pp20) cc_final: 0.7635 (pp20) REVERT: D 502 MET cc_start: 0.8641 (mtp) cc_final: 0.8220 (mtm) REVERT: D 687 GLN cc_start: 0.7043 (mp10) cc_final: 0.6602 (mp10) REVERT: D 753 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6621 (p0) REVERT: D 781 ARG cc_start: 0.7900 (ptm160) cc_final: 0.7093 (ptp90) REVERT: D 791 ASN cc_start: 0.7564 (m-40) cc_final: 0.6983 (m-40) REVERT: D 829 THR cc_start: 0.7627 (t) cc_final: 0.7106 (m) REVERT: D 965 GLN cc_start: 0.6846 (tp40) cc_final: 0.6352 (tp40) REVERT: D 969 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: D 1022 GLN cc_start: 0.7358 (mm-40) cc_final: 0.6508 (tm-30) outliers start: 172 outliers final: 117 residues processed: 838 average time/residue: 0.4894 time to fit residues: 651.3397 Evaluate side-chains 800 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 667 time to evaluate : 3.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 969 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 232 optimal weight: 20.0000 chunk 117 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 306 optimal weight: 0.0050 overall best weight: 2.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 395 HIS ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 395 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 623 GLN D 370 GLN D 395 HIS ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33468 Z= 0.213 Angle : 0.540 8.169 45660 Z= 0.279 Chirality : 0.044 0.176 4752 Planarity : 0.004 0.056 6036 Dihedral : 5.283 47.320 4456 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.06 % Allowed : 23.78 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: -0.19 (0.13), residues: 4036 helix: -0.03 (0.24), residues: 488 sheet: 0.67 (0.14), residues: 1360 loop : -0.64 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 654 HIS 0.005 0.001 HIS A 395 PHE 0.012 0.001 PHE C 225 TYR 0.025 0.002 TYR B 100 ARG 0.006 0.000 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 707 time to evaluate : 3.689 Fit side-chains REVERT: A 135 GLN cc_start: 0.7339 (mt0) cc_final: 0.6803 (mt0) REVERT: A 202 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8178 (pmm) REVERT: A 237 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.8048 (ttm-80) REVERT: A 264 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: A 388 ARG cc_start: 0.8687 (ttt180) cc_final: 0.8426 (ttt180) REVERT: A 438 GLU cc_start: 0.8024 (pp20) cc_final: 0.7617 (pp20) REVERT: A 502 MET cc_start: 0.8562 (mtp) cc_final: 0.8225 (mtm) REVERT: A 753 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6901 (p0) REVERT: A 781 ARG cc_start: 0.7968 (ptm160) cc_final: 0.7057 (ptp90) REVERT: A 791 ASN cc_start: 0.7567 (m-40) cc_final: 0.7120 (m110) REVERT: A 965 GLN cc_start: 0.6862 (tp40) cc_final: 0.6372 (tp40) REVERT: A 969 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: A 980 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6618 (mm-30) REVERT: A 1022 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6486 (tm-30) REVERT: B 33 PHE cc_start: 0.8297 (m-10) cc_final: 0.7399 (m-80) REVERT: B 202 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8063 (pmm) REVERT: B 237 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.8044 (ttm-80) REVERT: B 264 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: B 388 ARG cc_start: 0.8688 (ttt180) cc_final: 0.8424 (ttt180) REVERT: B 438 GLU cc_start: 0.8025 (pp20) cc_final: 0.7613 (pp20) REVERT: B 502 MET cc_start: 0.8626 (mtp) cc_final: 0.8256 (mtm) REVERT: B 753 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.6977 (p0) REVERT: B 781 ARG cc_start: 0.7963 (ptm160) cc_final: 0.7093 (ptp90) REVERT: B 791 ASN cc_start: 0.7551 (m-40) cc_final: 0.7106 (m110) REVERT: B 969 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: B 980 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6617 (mm-30) REVERT: B 1022 GLN cc_start: 0.7296 (mm-40) cc_final: 0.6489 (tm-30) REVERT: C 202 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8168 (pmm) REVERT: C 237 ARG cc_start: 0.8275 (ttm-80) cc_final: 0.8046 (ttm-80) REVERT: C 264 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: C 438 GLU cc_start: 0.8059 (pp20) cc_final: 0.7625 (pp20) REVERT: C 502 MET cc_start: 0.8526 (mtp) cc_final: 0.8173 (mtm) REVERT: C 753 ASN cc_start: 0.7136 (OUTLIER) cc_final: 0.6730 (p0) REVERT: C 781 ARG cc_start: 0.7977 (ptm160) cc_final: 0.7060 (ptp90) REVERT: C 791 ASN cc_start: 0.7556 (m-40) cc_final: 0.7080 (m-40) REVERT: C 829 THR cc_start: 0.7661 (t) cc_final: 0.7291 (p) REVERT: C 969 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: C 980 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6615 (mm-30) REVERT: C 1022 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6492 (tm-30) REVERT: D 202 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8065 (pmm) REVERT: D 237 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: D 264 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: D 388 ARG cc_start: 0.8689 (ttt180) cc_final: 0.8458 (ttt180) REVERT: D 420 MET cc_start: 0.8758 (mmt) cc_final: 0.8482 (mmt) REVERT: D 423 MET cc_start: 0.7896 (ttm) cc_final: 0.7620 (ttm) REVERT: D 436 MET cc_start: 0.8508 (ptp) cc_final: 0.8241 (ptp) REVERT: D 438 GLU cc_start: 0.8022 (pp20) cc_final: 0.7609 (pp20) REVERT: D 502 MET cc_start: 0.8589 (mtp) cc_final: 0.8219 (mtm) REVERT: D 687 GLN cc_start: 0.7061 (mp10) cc_final: 0.6607 (mp10) REVERT: D 753 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6586 (p0) REVERT: D 781 ARG cc_start: 0.7924 (ptm160) cc_final: 0.7070 (ptp90) REVERT: D 791 ASN cc_start: 0.7554 (m-40) cc_final: 0.7078 (m-40) REVERT: D 829 THR cc_start: 0.7650 (t) cc_final: 0.7092 (p) REVERT: D 952 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7891 (ttp-170) REVERT: D 965 GLN cc_start: 0.6855 (tp40) cc_final: 0.6358 (tp40) REVERT: D 969 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: D 980 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6667 (mm-30) REVERT: D 1022 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6492 (tm-30) outliers start: 175 outliers final: 137 residues processed: 827 average time/residue: 0.4812 time to fit residues: 630.9949 Evaluate side-chains 841 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 687 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 586 SER Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 804 ASN Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 952 ARG Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 985 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 7.9990 chunk 373 optimal weight: 0.6980 chunk 340 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 372 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 284 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 327 optimal weight: 9.9990 chunk 343 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 395 HIS A 719 GLN A 965 GLN B 226 HIS B 370 GLN B 395 HIS B 719 GLN ** B 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 719 GLN D 370 GLN D 395 HIS D 719 GLN D 965 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 33468 Z= 0.371 Angle : 0.614 8.742 45660 Z= 0.318 Chirality : 0.047 0.181 4752 Planarity : 0.005 0.057 6036 Dihedral : 5.632 48.634 4456 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 6.19 % Allowed : 23.06 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: -0.36 (0.13), residues: 4036 helix: -0.22 (0.23), residues: 488 sheet: 0.55 (0.14), residues: 1380 loop : -0.74 (0.14), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 720 HIS 0.007 0.001 HIS A 151 PHE 0.014 0.002 PHE A 225 TYR 0.028 0.002 TYR B 100 ARG 0.009 0.001 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 665 time to evaluate : 3.514 Fit side-chains REVERT: A 202 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8112 (pmm) REVERT: A 237 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.8050 (ttm-80) REVERT: A 487 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7029 (tm-30) REVERT: A 502 MET cc_start: 0.8672 (mtp) cc_final: 0.8282 (mtt) REVERT: A 753 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.6907 (p0) REVERT: A 781 ARG cc_start: 0.7913 (ptm160) cc_final: 0.7093 (ptp90) REVERT: A 791 ASN cc_start: 0.7583 (m-40) cc_final: 0.6978 (m-40) REVERT: A 965 GLN cc_start: 0.7004 (tp-100) cc_final: 0.6383 (tp40) REVERT: A 969 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: A 1022 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6483 (tm-30) REVERT: B 202 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8114 (pmm) REVERT: B 237 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.8057 (ttm-80) REVERT: B 473 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7828 (tpm-80) REVERT: B 487 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7073 (tm-30) REVERT: B 502 MET cc_start: 0.8676 (mtp) cc_final: 0.8275 (mtt) REVERT: B 753 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.6908 (p0) REVERT: B 781 ARG cc_start: 0.7977 (ptm160) cc_final: 0.7137 (ptp90) REVERT: B 791 ASN cc_start: 0.7570 (m-40) cc_final: 0.6968 (m-40) REVERT: B 952 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8025 (ttp-170) REVERT: B 965 GLN cc_start: 0.6927 (tp40) cc_final: 0.5938 (tp40) REVERT: B 969 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: B 1022 GLN cc_start: 0.7322 (mm-40) cc_final: 0.6485 (tm-30) REVERT: C 202 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8094 (pmm) REVERT: C 237 ARG cc_start: 0.8289 (ttm-80) cc_final: 0.8054 (ttm-80) REVERT: C 473 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7836 (tpm-80) REVERT: C 502 MET cc_start: 0.8657 (mtp) cc_final: 0.8238 (mtm) REVERT: C 753 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.6897 (p0) REVERT: C 781 ARG cc_start: 0.7918 (ptm160) cc_final: 0.7096 (ptp90) REVERT: C 791 ASN cc_start: 0.7571 (m-40) cc_final: 0.6963 (m-40) REVERT: C 969 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: C 1022 GLN cc_start: 0.7323 (mm-40) cc_final: 0.6485 (tm-30) REVERT: D 202 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8156 (pmm) REVERT: D 237 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.8036 (ttm-80) REVERT: D 436 MET cc_start: 0.8583 (ptp) cc_final: 0.8232 (ptp) REVERT: D 502 MET cc_start: 0.8684 (mtp) cc_final: 0.8305 (mtm) REVERT: D 654 TRP cc_start: 0.7346 (p90) cc_final: 0.7142 (p90) REVERT: D 753 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6754 (p0) REVERT: D 781 ARG cc_start: 0.7929 (ptm160) cc_final: 0.7120 (ptp90) REVERT: D 791 ASN cc_start: 0.7568 (m-40) cc_final: 0.6958 (m-40) REVERT: D 952 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7987 (ttp-170) REVERT: D 965 GLN cc_start: 0.7074 (tp-100) cc_final: 0.6458 (tp40) REVERT: D 969 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: D 1022 GLN cc_start: 0.7327 (mm-40) cc_final: 0.6486 (tm-30) outliers start: 214 outliers final: 166 residues processed: 817 average time/residue: 0.4733 time to fit residues: 614.0407 Evaluate side-chains 838 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 656 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 500 CYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 952 ARG Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 LYS Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 586 SER Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 952 ARG Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 985 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 chunk 383 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 182 optimal weight: 20.0000 chunk 266 optimal weight: 20.0000 chunk 402 optimal weight: 5.9990 chunk 370 optimal weight: 10.0000 chunk 320 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 247 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 395 HIS B 370 GLN B 395 HIS B 573 GLN ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 573 GLN ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 395 HIS D 573 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33468 Z= 0.228 Angle : 0.561 8.741 45660 Z= 0.290 Chirality : 0.045 0.179 4752 Planarity : 0.004 0.058 6036 Dihedral : 5.401 49.606 4456 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.18 % Allowed : 24.07 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: -0.28 (0.13), residues: 4036 helix: -0.12 (0.23), residues: 488 sheet: 0.60 (0.14), residues: 1360 loop : -0.69 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 654 HIS 0.005 0.001 HIS D 395 PHE 0.013 0.001 PHE A 225 TYR 0.025 0.002 TYR D 100 ARG 0.007 0.000 ARG B 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 671 time to evaluate : 4.275 Fit side-chains REVERT: A 135 GLN cc_start: 0.7405 (mt0) cc_final: 0.7109 (mt0) REVERT: A 202 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8162 (pmm) REVERT: A 237 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.8043 (ttm-80) REVERT: A 264 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: A 438 GLU cc_start: 0.8066 (pp20) cc_final: 0.7654 (pp20) REVERT: A 473 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7869 (tpm-80) REVERT: A 502 MET cc_start: 0.8617 (mtp) cc_final: 0.8244 (mtm) REVERT: A 753 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.6910 (p0) REVERT: A 781 ARG cc_start: 0.7906 (ptm160) cc_final: 0.7053 (ptp90) REVERT: A 791 ASN cc_start: 0.7561 (m-40) cc_final: 0.6942 (m-40) REVERT: A 965 GLN cc_start: 0.6944 (tp-100) cc_final: 0.6412 (tp40) REVERT: A 969 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: A 980 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6715 (mm-30) REVERT: A 1022 GLN cc_start: 0.7304 (mm-40) cc_final: 0.6493 (tm-30) REVERT: B 135 GLN cc_start: 0.6767 (mm110) cc_final: 0.6297 (mm-40) REVERT: B 202 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8150 (pmm) REVERT: B 237 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.8053 (ttm-80) REVERT: B 264 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: B 438 GLU cc_start: 0.8065 (pp20) cc_final: 0.7656 (pp20) REVERT: B 473 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7831 (tpm-80) REVERT: B 502 MET cc_start: 0.8643 (mtp) cc_final: 0.8225 (mtm) REVERT: B 753 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.6879 (p0) REVERT: B 781 ARG cc_start: 0.7964 (ptm160) cc_final: 0.7093 (ptp90) REVERT: B 791 ASN cc_start: 0.7548 (m-40) cc_final: 0.6929 (m-40) REVERT: B 965 GLN cc_start: 0.6903 (tp40) cc_final: 0.5909 (tp40) REVERT: B 969 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: B 980 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6712 (mm-30) REVERT: B 1022 GLN cc_start: 0.7308 (mm-40) cc_final: 0.6493 (tm-30) REVERT: C 202 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8117 (pmm) REVERT: C 237 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.8044 (ttm-80) REVERT: C 264 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: C 436 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8145 (ptp) REVERT: C 438 GLU cc_start: 0.8065 (pp20) cc_final: 0.7651 (pp20) REVERT: C 473 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7869 (tpm-80) REVERT: C 502 MET cc_start: 0.8485 (mtp) cc_final: 0.8122 (mtt) REVERT: C 753 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.7093 (p0) REVERT: C 781 ARG cc_start: 0.7913 (ptm160) cc_final: 0.7048 (ptp90) REVERT: C 791 ASN cc_start: 0.7553 (m-40) cc_final: 0.6930 (m-40) REVERT: C 969 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: C 980 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6711 (mm-30) REVERT: C 1022 GLN cc_start: 0.7310 (mm-40) cc_final: 0.6497 (tm-30) REVERT: D 202 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8168 (pmm) REVERT: D 237 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.8031 (ttm-80) REVERT: D 264 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: D 436 MET cc_start: 0.8442 (ptp) cc_final: 0.8089 (ptp) REVERT: D 438 GLU cc_start: 0.8065 (pp20) cc_final: 0.7651 (pp20) REVERT: D 502 MET cc_start: 0.8665 (mtp) cc_final: 0.8252 (mtt) REVERT: D 753 ASN cc_start: 0.7359 (OUTLIER) cc_final: 0.6951 (p0) REVERT: D 781 ARG cc_start: 0.7926 (ptm160) cc_final: 0.7040 (ptp90) REVERT: D 791 ASN cc_start: 0.7548 (m-40) cc_final: 0.6927 (m-40) REVERT: D 952 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7932 (ttp-170) REVERT: D 965 GLN cc_start: 0.6875 (tp-100) cc_final: 0.6333 (tp40) REVERT: D 969 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: D 1022 GLN cc_start: 0.7313 (mm-40) cc_final: 0.6494 (tm-30) outliers start: 179 outliers final: 152 residues processed: 793 average time/residue: 0.4714 time to fit residues: 592.7186 Evaluate side-chains 828 residues out of total 3456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 655 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 586 SER Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 ASN Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 473 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 500 CYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 648 ASP Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 753 ASN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 500 CYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 586 SER Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 LYS Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 753 ASN Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 905 ASN Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 500 CYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 586 SER Chi-restraints excluded: chain D residue 648 ASP Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 753 ASN Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 905 ASN Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 952 ARG Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 985 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 chunk 341 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 295 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 321 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 329 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 370 GLN A 395 HIS B 226 HIS B 370 GLN B 395 HIS B 573 GLN ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 370 GLN C 395 HIS C 573 GLN ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 370 GLN D 395 HIS D 573 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.136702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.120721 restraints weight = 46621.640| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.59 r_work: 0.3116 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 33468 Z= 0.227 Angle : 0.556 9.771 45660 Z= 0.287 Chirality : 0.045 0.177 4752 Planarity : 0.004 0.058 6036 Dihedral : 5.343 49.850 4456 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.53 % Allowed : 24.10 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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: -0.22 (0.13), residues: 4036 helix: -0.00 (0.24), residues: 488 sheet: 0.67 (0.14), residues: 1348 loop : -0.68 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 654 HIS 0.005 0.001 HIS C 395 PHE 0.013 0.001 PHE A 225 TYR 0.030 0.002 TYR D 100 ARG 0.006 0.000 ARG B 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9802.83 seconds wall clock time: 177 minutes 1.82 seconds (10621.82 seconds total)