Starting phenix.real_space_refine on Fri Mar 22 08:50:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/03_2024/3j7h_5995.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/03_2024/3j7h_5995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/03_2024/3j7h_5995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/03_2024/3j7h_5995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/03_2024/3j7h_5995.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/03_2024/3j7h_5995.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 156 5.16 5 C 20760 2.51 5 N 5808 2.21 5 O 6100 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A GLU 41": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 509": "OD1" <-> "OD2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 594": "OD1" <-> "OD2" Residue "A ASP 598": "OD1" <-> "OD2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 610": "OD1" <-> "OD2" Residue "A PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 659": "OD1" <-> "OD2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A ARG 894": "NH1" <-> "NH2" Residue "A PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 942": "NH1" <-> "NH2" Residue "A GLU 943": "OE1" <-> "OE2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 979": "OE1" <-> "OE2" Residue "A GLU 980": "OE1" <-> "OE2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 41": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B ARG 288": "NH1" <-> "NH2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 326": "OE1" <-> "OE2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 509": "OD1" <-> "OD2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 594": "OD1" <-> "OD2" Residue "B ASP 598": "OD1" <-> "OD2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 610": "OD1" <-> "OD2" Residue "B PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 659": "OD1" <-> "OD2" Residue "B PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 871": "OE1" <-> "OE2" Residue "B ARG 894": "NH1" <-> "NH2" Residue "B PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 942": "NH1" <-> "NH2" Residue "B GLU 943": "OE1" <-> "OE2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 979": "OE1" <-> "OE2" Residue "B GLU 980": "OE1" <-> "OE2" Residue "B PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 446": "NH1" <-> "NH2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 509": "OD1" <-> "OD2" Residue "C PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 594": "OD1" <-> "OD2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 610": "OD1" <-> "OD2" Residue "C PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 659": "OD1" <-> "OD2" Residue "C PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 871": "OE1" <-> "OE2" Residue "C ARG 894": "NH1" <-> "NH2" Residue "C PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 942": "NH1" <-> "NH2" Residue "C GLU 943": "OE1" <-> "OE2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 979": "OE1" <-> "OE2" Residue "C GLU 980": "OE1" <-> "OE2" Residue "C PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 446": "NH1" <-> "NH2" Residue "D TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 509": "OD1" <-> "OD2" Residue "D PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 594": "OD1" <-> "OD2" Residue "D ASP 598": "OD1" <-> "OD2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 610": "OD1" <-> "OD2" Residue "D PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 659": "OD1" <-> "OD2" Residue "D PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 871": "OE1" <-> "OE2" Residue "D ARG 894": "NH1" <-> "NH2" Residue "D PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 942": "NH1" <-> "NH2" Residue "D GLU 943": "OE1" <-> "OE2" Residue "D ARG 952": "NH1" <-> "NH2" Residue "D PHE 955": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 979": "OE1" <-> "OE2" Residue "D GLU 980": "OE1" <-> "OE2" Residue "D PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1016": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32828 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 11, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 948} Chain: "B" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 11, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 948} Chain: "C" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 11, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 948} Chain: "D" Number of atoms: 8206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 8206 Classifications: {'peptide': 1022} Link IDs: {'CIS': 11, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 948} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.15, per 1000 atoms: 0.52 Number of scatterers: 32828 At special positions: 0 Unit cell: (191.887, 147.262, 100.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 Mg 4 11.99 O 6100 8.00 N 5808 7.00 C 20760 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: 13.86 Conformation dependent library (CDL) restraints added in 6.0 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7608 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 52 sheets defined 16.8% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.14 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.728A pdb=" N ALA A 42 " --> pdb=" O ASN A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.545A pdb=" N LEU A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.732A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 368 through 382 removed outlier: 3.556A pdb=" N MET A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.812A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.513A pdb=" N GLU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 445 " --> pdb=" O THR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.574A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 526 removed outlier: 3.693A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.576A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.819A pdb=" N PHE A 601 " --> pdb=" O ASP A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 removed outlier: 4.014A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 4.099A 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 922 through 926 removed outlier: 4.107A pdb=" N TYR A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 922 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'B' and resid 6 through 12 Processing helix chain 'B' and resid 38 through 45 removed outlier: 3.728A pdb=" N ALA B 42 " --> pdb=" O ASN B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 removed outlier: 3.544A pdb=" N LEU B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.732A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 368 through 382 removed outlier: 3.557A pdb=" N MET B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 373 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.812A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'B' and resid 432 through 448 removed outlier: 3.513A pdb=" N GLU B 438 " --> pdb=" O PRO B 434 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 445 " --> pdb=" O THR B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.574A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 526 removed outlier: 3.693A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.576A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.819A pdb=" N PHE B 601 " --> pdb=" O ASP B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 removed outlier: 4.013A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 4.100A 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 922 through 926 removed outlier: 4.107A pdb=" N TYR B 926 " --> pdb=" O LEU B 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 922 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 38 through 45 removed outlier: 3.729A pdb=" N ALA C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.545A pdb=" N LEU C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.732A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 368 through 382 removed outlier: 3.556A pdb=" N MET C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 373 " --> pdb=" O GLU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.813A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 432 through 448 removed outlier: 3.512A pdb=" N GLU C 438 " --> pdb=" O PRO C 434 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 440 " --> pdb=" O MET C 436 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.574A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 526 removed outlier: 3.693A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.575A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 603 removed outlier: 3.819A pdb=" N PHE C 601 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 removed outlier: 4.014A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 4.099A 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 922 through 926 removed outlier: 4.108A pdb=" N TYR C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 922 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'D' and resid 6 through 12 Processing helix chain 'D' and resid 38 through 45 removed outlier: 3.729A pdb=" N ALA D 42 " --> pdb=" O ASN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.545A pdb=" N LEU D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.732A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.556A pdb=" N MET D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.812A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 432 through 448 removed outlier: 3.512A pdb=" N GLU D 438 " --> pdb=" O PRO D 434 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 440 " --> pdb=" O MET D 436 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN D 445 " --> pdb=" O THR D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.574A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 526 removed outlier: 3.694A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.576A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.819A pdb=" N PHE D 601 " --> pdb=" O ASP D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 removed outlier: 4.014A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 4.099A 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 922 through 926 removed outlier: 4.106A pdb=" N TYR D 926 " --> pdb=" O LEU D 922 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 922 through 926' Processing helix chain 'D' and resid 963 through 970 Processing sheet with id= A, first strand: chain 'A' and resid 52 through 53 Processing sheet with id= B, first strand: chain 'A' and resid 83 through 86 removed outlier: 3.604A pdb=" N GLY A 56 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 129 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 222 through 231 Processing sheet with id= D, first strand: chain 'A' and resid 265 through 273 removed outlier: 4.645A pdb=" N GLN A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN A 262 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 268 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 335 through 338 Processing sheet with id= F, first strand: chain 'A' and resid 453 through 457 removed outlier: 7.795A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 389 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY A 353 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 511 through 512 Processing sheet with id= H, first strand: chain 'A' and resid 575 through 578 Processing sheet with id= I, first strand: chain 'A' and resid 628 through 632 Processing sheet with id= J, first strand: chain 'A' and resid 661 through 670 removed outlier: 5.864A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU A 650 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 739 through 742 removed outlier: 3.545A pdb=" N GLN A 767 " --> pdb=" O GLN A 757 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.749A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 781 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.701A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.254A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.749A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 781 " --> pdb=" O ASN A 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 899 " --> pdb=" O ASP A 916 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 914 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 52 through 53 Processing sheet with id= O, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.604A pdb=" N GLY B 56 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL B 129 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 222 through 231 Processing sheet with id= Q, first strand: chain 'B' and resid 265 through 273 removed outlier: 4.645A pdb=" N GLN B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN B 262 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 268 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 335 through 338 Processing sheet with id= S, first strand: chain 'B' and resid 453 through 457 removed outlier: 7.795A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS B 389 " --> pdb=" O VAL B 410 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY B 353 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 511 through 512 Processing sheet with id= U, first strand: chain 'B' and resid 575 through 578 Processing sheet with id= V, first strand: chain 'B' and resid 628 through 632 Processing sheet with id= W, first strand: chain 'B' and resid 661 through 670 removed outlier: 5.864A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU B 650 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 739 through 742 removed outlier: 3.545A pdb=" N GLN B 767 " --> pdb=" O GLN B 757 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.748A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 781 " --> pdb=" O ASN B 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.187A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.701A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.254A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.748A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 781 " --> pdb=" O ASN B 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.187A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 899 " --> pdb=" O ASP B 916 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS B 914 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 52 through 53 Processing sheet with id= AB, first strand: chain 'C' and resid 83 through 86 removed outlier: 3.604A pdb=" N GLY C 56 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL C 129 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 222 through 231 Processing sheet with id= AD, first strand: chain 'C' and resid 265 through 273 removed outlier: 4.645A pdb=" N GLN C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLN C 262 " --> pdb=" O GLN C 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 268 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 335 through 338 Processing sheet with id= AF, first strand: chain 'C' and resid 453 through 457 removed outlier: 7.795A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS C 389 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 353 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 511 through 512 Processing sheet with id= AH, first strand: chain 'C' and resid 575 through 578 Processing sheet with id= AI, first strand: chain 'C' and resid 628 through 632 Processing sheet with id= AJ, first strand: chain 'C' and resid 661 through 670 removed outlier: 5.864A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 650 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 739 through 742 removed outlier: 3.545A pdb=" N GLN C 767 " --> pdb=" O GLN C 757 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.749A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 781 " --> pdb=" O ASN C 885 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.591A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.701A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.254A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.749A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 781 " --> pdb=" O ASN C 885 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 899 " --> pdb=" O ASP C 916 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 914 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'D' and resid 52 through 53 Processing sheet with id= AO, first strand: chain 'D' and resid 83 through 86 removed outlier: 3.604A pdb=" N GLY D 56 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 129 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'D' and resid 222 through 231 Processing sheet with id= AQ, first strand: chain 'D' and resid 265 through 273 removed outlier: 4.644A pdb=" N GLN D 266 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLN D 262 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA D 268 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'D' and resid 335 through 338 Processing sheet with id= AS, first strand: chain 'D' and resid 453 through 457 removed outlier: 7.795A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS D 389 " --> pdb=" O VAL D 410 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY D 353 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'D' and resid 511 through 512 Processing sheet with id= AU, first strand: chain 'D' and resid 575 through 578 Processing sheet with id= AV, first strand: chain 'D' and resid 628 through 632 Processing sheet with id= AW, first strand: chain 'D' and resid 661 through 670 removed outlier: 5.864A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU D 650 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'D' and resid 739 through 742 removed outlier: 3.545A pdb=" N GLN D 767 " --> pdb=" O GLN D 757 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.748A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 781 " --> pdb=" O ASN D 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.591A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.701A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.255A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.561A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.748A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D 781 " --> pdb=" O ASN D 885 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.188A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 899 " --> pdb=" O ASP D 916 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS D 914 " --> pdb=" O GLY D 901 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3288 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: 15.07 Time building geometry restraints manager: 14.88 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: 11076 1.34 - 1.46: 7356 1.46 - 1.58: 15112 1.58 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 33792 Sorted by residual: bond pdb=" C ASN B 110 " pdb=" N PRO B 111 " ideal model delta sigma weight residual 1.329 1.407 -0.078 1.18e-02 7.18e+03 4.33e+01 bond pdb=" C ASN D 110 " pdb=" N PRO D 111 " ideal model delta sigma weight residual 1.329 1.407 -0.078 1.18e-02 7.18e+03 4.33e+01 bond pdb=" C ASN C 110 " pdb=" N PRO C 111 " ideal model delta sigma weight residual 1.329 1.407 -0.078 1.18e-02 7.18e+03 4.33e+01 bond pdb=" C ASN A 110 " pdb=" N PRO A 111 " ideal model delta sigma weight residual 1.329 1.407 -0.078 1.18e-02 7.18e+03 4.33e+01 bond pdb=" C ILE A 305 " pdb=" N PRO A 306 " ideal model delta sigma weight residual 1.335 1.408 -0.073 1.36e-02 5.41e+03 2.85e+01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 100.62 - 108.58: 2575 108.58 - 116.53: 21502 116.53 - 124.49: 21078 124.49 - 132.45: 777 132.45 - 140.41: 172 Bond angle restraints: 46104 Sorted by residual: angle pdb=" N ASP D 610 " pdb=" CA ASP D 610 " pdb=" C ASP D 610 " ideal model delta sigma weight residual 111.71 120.08 -8.37 1.15e+00 7.56e-01 5.29e+01 angle pdb=" N ASP B 610 " pdb=" CA ASP B 610 " pdb=" C ASP B 610 " ideal model delta sigma weight residual 111.71 120.06 -8.35 1.15e+00 7.56e-01 5.28e+01 angle pdb=" N ASP C 610 " pdb=" CA ASP C 610 " pdb=" C ASP C 610 " ideal model delta sigma weight residual 111.71 120.06 -8.35 1.15e+00 7.56e-01 5.28e+01 angle pdb=" N ASP A 610 " pdb=" CA ASP A 610 " pdb=" C ASP A 610 " ideal model delta sigma weight residual 111.71 120.06 -8.35 1.15e+00 7.56e-01 5.28e+01 angle pdb=" N TYR D 405 " pdb=" CA TYR D 405 " pdb=" C TYR D 405 " ideal model delta sigma weight residual 111.14 118.93 -7.79 1.08e+00 8.57e-01 5.20e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 16973 17.81 - 35.61: 1923 35.61 - 53.42: 662 53.42 - 71.23: 194 71.23 - 89.03: 48 Dihedral angle restraints: 19800 sinusoidal: 7984 harmonic: 11816 Sorted by residual: dihedral pdb=" CA ASN C 147 " pdb=" C ASN C 147 " pdb=" N SER C 148 " pdb=" CA SER C 148 " ideal model delta harmonic sigma weight residual 0.00 -24.35 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ASN D 147 " pdb=" C ASN D 147 " pdb=" N SER D 148 " pdb=" CA SER D 148 " ideal model delta harmonic sigma weight residual 0.00 -24.31 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ASN A 147 " pdb=" C ASN A 147 " pdb=" N SER A 148 " pdb=" CA SER A 148 " ideal model delta harmonic sigma weight residual 0.00 -24.31 24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 19797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3374 0.058 - 0.117: 1033 0.117 - 0.175: 342 0.175 - 0.234: 55 0.234 - 0.292: 16 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CA ASP B 610 " pdb=" N ASP B 610 " pdb=" C ASP B 610 " pdb=" CB ASP B 610 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ASP A 610 " pdb=" N ASP A 610 " pdb=" C ASP A 610 " pdb=" CB ASP A 610 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ASP C 610 " pdb=" N ASP C 610 " pdb=" C ASP C 610 " pdb=" CB ASP C 610 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 4817 not shown) Planarity restraints: 6088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 510 " -0.092 5.00e-02 4.00e+02 1.44e-01 3.31e+01 pdb=" N PRO A 511 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO A 511 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO A 511 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 510 " 0.092 5.00e-02 4.00e+02 1.44e-01 3.30e+01 pdb=" N PRO B 511 " -0.249 5.00e-02 4.00e+02 pdb=" CA PRO B 511 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO B 511 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 510 " -0.092 5.00e-02 4.00e+02 1.44e-01 3.30e+01 pdb=" N PRO D 511 " 0.249 5.00e-02 4.00e+02 pdb=" CA PRO D 511 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO D 511 " -0.073 5.00e-02 4.00e+02 ... (remaining 6085 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 174 1.85 - 2.61: 2033 2.61 - 3.37: 46339 3.37 - 4.14: 85478 4.14 - 4.90: 154792 Nonbonded interactions: 288816 Sorted by model distance: nonbonded pdb=" CD2 HIS A 391 " pdb=" OD1 ASN A 460 " model vdw 1.085 3.260 nonbonded pdb=" CD2 HIS C 391 " pdb=" OD1 ASN C 460 " model vdw 1.085 3.260 nonbonded pdb=" CD2 HIS D 391 " pdb=" OD1 ASN D 460 " model vdw 1.085 3.260 nonbonded pdb=" CD2 HIS B 391 " pdb=" OD1 ASN B 460 " model vdw 1.086 3.260 nonbonded pdb=" ND1 HIS C1015 " pdb=" ND1 HIS D1015 " model vdw 1.110 3.200 ... (remaining 288811 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.000 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 90.510 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.005 0.078 33792 Z= 0.310 Angle : 1.168 15.411 46104 Z= 0.820 Chirality : 0.064 0.292 4820 Planarity : 0.012 0.144 6088 Dihedral : 17.984 89.033 12192 Min Nonbonded Distance : 1.085 Molprobity Statistics. All-atom Clashscore : 132.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.45 % Favored : 97.35 % Rotamer: Outliers : 12.24 % Allowed : 20.68 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.13), residues: 4080 helix: 2.48 (0.20), residues: 516 sheet: 3.21 (0.14), residues: 1272 loop : 0.43 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 553 HIS 0.003 0.001 HIS B 815 PHE 0.009 0.001 PHE A 957 TYR 0.008 0.001 TYR B 105 ARG 0.002 0.000 ARG D 800 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 428 poor density : 782 time to evaluate : 3.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7777 (p90) REVERT: A 166 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7179 (mmt180) REVERT: A 170 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: A 210 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.6808 (mtt180) REVERT: A 246 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6940 (ptp) REVERT: A 542 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6162 (ttm) REVERT: A 881 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.6797 (ptp-170) REVERT: A 1013 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7393 (mtm-85) REVERT: B 90 TRP cc_start: 0.8164 (OUTLIER) cc_final: 0.7694 (p90) REVERT: B 166 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7194 (mmt180) REVERT: B 170 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: B 210 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6790 (mtt180) REVERT: B 246 MET cc_start: 0.7265 (OUTLIER) cc_final: 0.6923 (ptp) REVERT: B 542 MET cc_start: 0.6417 (OUTLIER) cc_final: 0.6168 (ttm) REVERT: B 881 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6836 (ptp-170) REVERT: B 1013 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7378 (mtm-85) REVERT: C 90 TRP cc_start: 0.8193 (OUTLIER) cc_final: 0.7767 (p90) REVERT: C 166 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7209 (mmt180) REVERT: C 170 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: C 210 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.6779 (mtt180) REVERT: C 246 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6933 (ptp) REVERT: C 542 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.6190 (ttm) REVERT: C 881 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6715 (ptp-170) REVERT: C 1013 ARG cc_start: 0.7776 (ttm-80) cc_final: 0.7361 (mtm-85) REVERT: D 90 TRP cc_start: 0.8175 (OUTLIER) cc_final: 0.7753 (p90) REVERT: D 166 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7196 (mmt180) REVERT: D 170 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6114 (mp0) REVERT: D 210 ARG cc_start: 0.7556 (OUTLIER) cc_final: 0.6796 (mtt180) REVERT: D 246 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6923 (ptp) REVERT: D 542 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6217 (ttm) REVERT: D 881 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6742 (ptp-170) REVERT: D 1013 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7363 (mtm-85) outliers start: 428 outliers final: 206 residues processed: 1150 average time/residue: 0.5101 time to fit residues: 890.5986 Evaluate side-chains 654 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 420 time to evaluate : 3.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 90 TRP Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 221 GLN Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 439 ARG Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 601 PHE Chi-restraints excluded: chain A residue 603 MET Chi-restraints excluded: chain A residue 604 ASN Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 786 ARG Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 881 ARG Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 962 TYR Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1009 LEU Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 255 ARG Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 391 HIS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 542 MET Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 601 PHE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain B residue 767 GLN Chi-restraints excluded: chain B residue 786 ARG Chi-restraints excluded: chain B residue 815 HIS Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 876 THR Chi-restraints excluded: chain B residue 881 ARG Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 962 TYR Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1009 LEU Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 90 TRP Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 221 GLN Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 266 GLN Chi-restraints excluded: chain C residue 274 PHE Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 375 ASP Chi-restraints excluded: chain C residue 380 LYS Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 439 ARG Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 542 MET Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 601 PHE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 604 ASN Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 767 GLN Chi-restraints excluded: chain C residue 786 ARG Chi-restraints excluded: chain C residue 815 HIS Chi-restraints excluded: chain C residue 850 PHE Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 881 ARG Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 962 TYR Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1009 LEU Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 90 TRP Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 221 GLN Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 251 ARG Chi-restraints excluded: chain D residue 255 ARG Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 380 LYS Chi-restraints excluded: chain D residue 391 HIS Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 ARG Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 542 MET Chi-restraints excluded: chain D residue 592 PHE Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 601 PHE Chi-restraints excluded: chain D residue 603 MET Chi-restraints excluded: chain D residue 604 ASN Chi-restraints excluded: chain D residue 606 LEU Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 767 GLN Chi-restraints excluded: chain D residue 786 ARG Chi-restraints excluded: chain D residue 815 HIS Chi-restraints excluded: chain D residue 850 PHE Chi-restraints excluded: chain D residue 876 THR Chi-restraints excluded: chain D residue 881 ARG Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 962 TYR Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1008 GLN Chi-restraints excluded: chain D residue 1009 LEU Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 208 optimal weight: 0.3980 chunk 165 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 238 optimal weight: 0.4980 chunk 370 optimal weight: 10.0000 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 30 HIS A 50 GLN ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 163 GLN A 221 GLN A 226 HIS A 245 GLN A 266 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 468 HIS A 573 GLN A 624 GLN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 ASN ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 878 HIS ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN B 18 ASN B 30 HIS B 50 GLN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 163 GLN B 221 GLN B 226 HIS B 245 GLN B 266 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 468 HIS B 573 GLN B 624 GLN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 HIS ** B 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 ASN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 844 HIS B 878 HIS ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 GLN C 18 ASN C 30 HIS C 50 GLN ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS C 163 GLN C 221 GLN C 226 HIS C 245 GLN C 266 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 468 HIS C 573 GLN C 624 GLN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 HIS ** C 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 ASN C 739 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 878 HIS ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 GLN D 18 ASN D 30 HIS D 50 GLN ** D 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 HIS D 163 GLN D 221 GLN D 226 HIS D 245 GLN D 266 GLN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 468 HIS D 573 GLN D 624 GLN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS ** D 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 725 ASN ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 878 HIS ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1022 GLN Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33792 Z= 0.351 Angle : 0.761 12.563 46104 Z= 0.407 Chirality : 0.049 0.179 4820 Planarity : 0.007 0.061 6088 Dihedral : 11.364 87.330 5056 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 7.04 % Allowed : 21.28 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4080 helix: 0.92 (0.21), residues: 556 sheet: 2.23 (0.14), residues: 1284 loop : 0.03 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 769 HIS 0.019 0.002 HIS B 30 PHE 0.022 0.003 PHE A 764 TYR 0.019 0.002 TYR D 503 ARG 0.009 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 423 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7934 (mtp-110) REVERT: A 280 ASP cc_start: 0.5715 (p0) cc_final: 0.5489 (p0) REVERT: A 428 ASP cc_start: 0.6866 (t70) cc_final: 0.6646 (t0) REVERT: A 1013 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7468 (mtm-85) REVERT: B 237 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7922 (mtp-110) REVERT: B 280 ASP cc_start: 0.5739 (p0) cc_final: 0.5501 (p0) REVERT: B 428 ASP cc_start: 0.6875 (t70) cc_final: 0.6667 (t0) REVERT: B 884 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7736 (pp) REVERT: B 1013 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7458 (mtm-85) REVERT: C 237 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7926 (mtp-110) REVERT: C 884 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7702 (pp) REVERT: C 1013 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7457 (mtm-85) REVERT: D 237 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7925 (mtp-110) REVERT: D 1013 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7464 (mtm-85) outliers start: 246 outliers final: 140 residues processed: 614 average time/residue: 0.4797 time to fit residues: 461.9466 Evaluate side-chains 477 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 335 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 624 GLN Chi-restraints excluded: chain A residue 708 TRP Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 624 GLN Chi-restraints excluded: chain B residue 708 TRP Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 624 GLN Chi-restraints excluded: chain C residue 708 TRP Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1008 GLN Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 259 SER Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 624 GLN Chi-restraints excluded: chain D residue 708 TRP Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 5.9990 chunk 400 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 0.0010 overall best weight: 3.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 563 GLN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS B 563 GLN ** B 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 563 GLN ** C 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 HIS D 563 GLN ** D 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 33792 Z= 0.304 Angle : 0.655 10.922 46104 Z= 0.347 Chirality : 0.046 0.188 4820 Planarity : 0.005 0.048 6088 Dihedral : 7.321 59.743 4576 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 7.89 % Allowed : 19.77 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: 0.85 (0.13), residues: 4080 helix: 0.60 (0.22), residues: 556 sheet: 1.99 (0.14), residues: 1272 loop : -0.28 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 769 HIS 0.008 0.001 HIS B 391 PHE 0.016 0.002 PHE A 209 TYR 0.015 0.002 TYR D 105 ARG 0.009 0.001 ARG D 442 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 355 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.6040 (p0) cc_final: 0.5791 (p0) REVERT: A 521 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7809 (mttt) REVERT: A 572 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6351 (m-30) REVERT: A 702 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7255 (mp-120) REVERT: A 1020 TRP cc_start: 0.8025 (OUTLIER) cc_final: 0.7241 (t60) REVERT: B 280 ASP cc_start: 0.6090 (p0) cc_final: 0.5833 (p0) REVERT: B 521 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7771 (mttt) REVERT: B 572 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6345 (m-30) REVERT: B 702 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7248 (mp-120) REVERT: B 1020 TRP cc_start: 0.8025 (OUTLIER) cc_final: 0.7238 (t60) REVERT: C 280 ASP cc_start: 0.6089 (p0) cc_final: 0.5821 (p0) REVERT: C 323 ILE cc_start: 0.7807 (mp) cc_final: 0.7456 (mt) REVERT: C 521 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7797 (mttt) REVERT: C 572 ASP cc_start: 0.6693 (OUTLIER) cc_final: 0.6368 (m-30) REVERT: C 702 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7284 (mp-120) REVERT: C 1020 TRP cc_start: 0.8023 (OUTLIER) cc_final: 0.7264 (t60) REVERT: D 280 ASP cc_start: 0.6048 (p0) cc_final: 0.5802 (p0) REVERT: D 323 ILE cc_start: 0.7822 (mp) cc_final: 0.7466 (mt) REVERT: D 521 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7801 (mttt) REVERT: D 572 ASP cc_start: 0.6691 (OUTLIER) cc_final: 0.6371 (m-30) REVERT: D 702 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7280 (mp-120) REVERT: D 768 MET cc_start: 0.6868 (ttm) cc_final: 0.6643 (ttm) REVERT: D 1020 TRP cc_start: 0.8016 (OUTLIER) cc_final: 0.7221 (t60) outliers start: 276 outliers final: 143 residues processed: 582 average time/residue: 0.4640 time to fit residues: 426.2638 Evaluate side-chains 455 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 296 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 521 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 389 CYS Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 743 SER Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 7.9990 chunk 394 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 353 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN A 394 ASN A 625 GLN A 646 HIS ** A 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 394 ASN B 625 GLN B 646 HIS ** B 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 625 GLN C 646 HIS ** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 863 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 625 GLN ** D 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 863 GLN ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 33792 Z= 0.397 Angle : 0.673 11.983 46104 Z= 0.356 Chirality : 0.047 0.240 4820 Planarity : 0.005 0.051 6088 Dihedral : 6.677 59.862 4536 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 8.01 % Allowed : 20.65 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: 0.40 (0.13), residues: 4080 helix: -0.19 (0.21), residues: 604 sheet: 1.25 (0.14), residues: 1416 loop : -0.25 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 90 HIS 0.006 0.001 HIS D 391 PHE 0.019 0.002 PHE C 747 TYR 0.014 0.002 TYR D 105 ARG 0.005 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 326 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.6068 (p0) cc_final: 0.5797 (p0) REVERT: A 521 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7959 (mttt) REVERT: A 572 ASP cc_start: 0.6628 (OUTLIER) cc_final: 0.6266 (m-30) REVERT: A 684 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: A 702 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7272 (mp-120) REVERT: A 719 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: A 1020 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.7254 (t60) REVERT: B 280 ASP cc_start: 0.6096 (p0) cc_final: 0.5835 (p0) REVERT: B 521 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7899 (mttt) REVERT: B 572 ASP cc_start: 0.6620 (OUTLIER) cc_final: 0.6260 (m-30) REVERT: B 684 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: B 702 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7265 (mp-120) REVERT: B 719 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: B 1020 TRP cc_start: 0.7983 (OUTLIER) cc_final: 0.7274 (t60) REVERT: C 280 ASP cc_start: 0.6045 (p0) cc_final: 0.5767 (p0) REVERT: C 323 ILE cc_start: 0.7873 (mp) cc_final: 0.7511 (mt) REVERT: C 521 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7954 (mttt) REVERT: C 572 ASP cc_start: 0.6631 (OUTLIER) cc_final: 0.6268 (m-30) REVERT: C 684 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7026 (mt-10) REVERT: C 702 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7275 (mp-120) REVERT: C 719 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7310 (tm-30) REVERT: C 1020 TRP cc_start: 0.7972 (OUTLIER) cc_final: 0.7274 (t60) REVERT: D 280 ASP cc_start: 0.6026 (p0) cc_final: 0.5758 (p0) REVERT: D 323 ILE cc_start: 0.7877 (mp) cc_final: 0.7514 (mt) REVERT: D 521 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7950 (mttt) REVERT: D 572 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.6270 (m-30) REVERT: D 684 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: D 702 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7275 (mp-120) REVERT: D 719 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: D 1020 TRP cc_start: 0.7959 (OUTLIER) cc_final: 0.7248 (t60) outliers start: 280 outliers final: 182 residues processed: 565 average time/residue: 0.4482 time to fit residues: 416.6444 Evaluate side-chains 497 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 291 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 521 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 611 ARG Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 521 LYS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 521 LYS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 611 ARG Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 743 SER Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 863 GLN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 863 GLN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 646 HIS ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 33792 Z= 0.320 Angle : 0.634 11.958 46104 Z= 0.333 Chirality : 0.045 0.231 4820 Planarity : 0.004 0.047 6088 Dihedral : 6.365 59.735 4536 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 7.89 % Allowed : 20.42 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: 0.25 (0.13), residues: 4080 helix: -0.04 (0.22), residues: 580 sheet: 1.07 (0.14), residues: 1412 loop : -0.37 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 553 HIS 0.005 0.001 HIS A 391 PHE 0.025 0.002 PHE A1007 TYR 0.012 0.002 TYR C 399 ARG 0.006 0.001 ARG D 894 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 332 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.6045 (p0) cc_final: 0.5804 (p0) REVERT: A 572 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6215 (m-30) REVERT: A 702 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7311 (mp-120) REVERT: A 719 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: A 996 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6322 (m-30) REVERT: B 280 ASP cc_start: 0.6064 (p0) cc_final: 0.5824 (p0) REVERT: B 572 ASP cc_start: 0.6476 (OUTLIER) cc_final: 0.6205 (m-30) REVERT: B 702 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7315 (mp-120) REVERT: B 719 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: B 996 ASP cc_start: 0.6800 (OUTLIER) cc_final: 0.6291 (m-30) REVERT: C 280 ASP cc_start: 0.6003 (p0) cc_final: 0.5710 (p0) REVERT: C 323 ILE cc_start: 0.7841 (mp) cc_final: 0.7565 (mt) REVERT: C 572 ASP cc_start: 0.6494 (OUTLIER) cc_final: 0.6217 (m-30) REVERT: C 702 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7336 (mp-120) REVERT: C 719 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: C 996 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6286 (m-30) REVERT: C 1020 TRP cc_start: 0.7962 (OUTLIER) cc_final: 0.7275 (t60) REVERT: D 280 ASP cc_start: 0.5976 (p0) cc_final: 0.5705 (p0) REVERT: D 323 ILE cc_start: 0.7856 (mp) cc_final: 0.7548 (mt) REVERT: D 572 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6217 (m-30) REVERT: D 702 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7322 (mp-120) REVERT: D 719 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: D 996 ASP cc_start: 0.6834 (OUTLIER) cc_final: 0.6298 (m-30) REVERT: D 1020 TRP cc_start: 0.7979 (OUTLIER) cc_final: 0.7251 (t60) outliers start: 276 outliers final: 186 residues processed: 565 average time/residue: 0.4408 time to fit residues: 405.5004 Evaluate side-chains 504 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 300 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 262 GLN Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 262 GLN Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 262 GLN Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 520 ILE Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 743 SER Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 894 ARG Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.4980 chunk 355 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 33792 Z= 0.376 Angle : 0.654 12.010 46104 Z= 0.343 Chirality : 0.046 0.262 4820 Planarity : 0.005 0.048 6088 Dihedral : 6.161 59.962 4520 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 7.58 % Allowed : 21.37 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: 0.02 (0.13), residues: 4080 helix: -0.12 (0.22), residues: 588 sheet: 0.80 (0.14), residues: 1432 loop : -0.45 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 90 HIS 0.004 0.001 HIS D 391 PHE 0.018 0.002 PHE B 209 TYR 0.011 0.002 TYR D 399 ARG 0.006 0.001 ARG D 894 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 325 time to evaluate : 3.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ASP cc_start: 0.6020 (p0) cc_final: 0.5719 (p0) REVERT: A 572 ASP cc_start: 0.6518 (OUTLIER) cc_final: 0.6222 (m-30) REVERT: A 655 MET cc_start: 0.8942 (ptt) cc_final: 0.8674 (ptp) REVERT: A 684 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7026 (mt-10) REVERT: A 702 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7346 (mp-120) REVERT: A 719 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: A 996 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6331 (m-30) REVERT: A 1020 TRP cc_start: 0.7977 (OUTLIER) cc_final: 0.7243 (t60) REVERT: B 280 ASP cc_start: 0.6065 (p0) cc_final: 0.5756 (p0) REVERT: B 572 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.6195 (m-30) REVERT: B 655 MET cc_start: 0.8937 (ptt) cc_final: 0.8663 (ptp) REVERT: B 684 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: B 702 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7355 (mp-120) REVERT: B 719 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: B 996 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.6311 (m-30) REVERT: C 237 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7739 (ttp-110) REVERT: C 280 ASP cc_start: 0.6022 (p0) cc_final: 0.5703 (p0) REVERT: C 323 ILE cc_start: 0.7936 (mp) cc_final: 0.7596 (mt) REVERT: C 572 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.6205 (m-30) REVERT: C 655 MET cc_start: 0.8935 (ptt) cc_final: 0.8672 (ptp) REVERT: C 684 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: C 702 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7354 (mp-120) REVERT: C 719 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: C 996 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6312 (m-30) REVERT: C 1020 TRP cc_start: 0.7984 (OUTLIER) cc_final: 0.7283 (t60) REVERT: D 237 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7737 (ttp-110) REVERT: D 280 ASP cc_start: 0.6010 (p0) cc_final: 0.5718 (p0) REVERT: D 323 ILE cc_start: 0.7929 (mp) cc_final: 0.7590 (mt) REVERT: D 572 ASP cc_start: 0.6519 (OUTLIER) cc_final: 0.6213 (m-30) REVERT: D 655 MET cc_start: 0.8941 (ptt) cc_final: 0.8684 (ptp) REVERT: D 684 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: D 702 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7353 (mp-120) REVERT: D 719 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: D 996 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6296 (m-30) REVERT: D 1020 TRP cc_start: 0.7977 (OUTLIER) cc_final: 0.7283 (t60) outliers start: 265 outliers final: 198 residues processed: 545 average time/residue: 0.4605 time to fit residues: 415.3149 Evaluate side-chains 527 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 304 time to evaluate : 3.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 965 GLN Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 509 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 103 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 743 SER Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 780 LEU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 894 ARG Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 965 GLN Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 393 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 GLN A 863 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN B 394 ASN ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 394 ASN C 863 GLN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 33792 Z= 0.302 Angle : 0.626 11.844 46104 Z= 0.327 Chirality : 0.045 0.210 4820 Planarity : 0.004 0.045 6088 Dihedral : 5.944 59.793 4514 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 7.21 % Allowed : 22.60 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: 0.05 (0.13), residues: 4080 helix: 0.03 (0.23), residues: 564 sheet: 0.74 (0.14), residues: 1412 loop : -0.41 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 553 HIS 0.005 0.001 HIS B 395 PHE 0.018 0.002 PHE B1007 TYR 0.011 0.002 TYR B1014 ARG 0.006 0.001 ARG D 894 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 322 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7659 (ttp-110) REVERT: A 280 ASP cc_start: 0.6026 (p0) cc_final: 0.5724 (p0) REVERT: A 492 ASP cc_start: 0.6614 (p0) cc_final: 0.6336 (p0) REVERT: A 572 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6208 (m-30) REVERT: A 684 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6979 (mt-10) REVERT: A 702 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7341 (mp-120) REVERT: A 719 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: A 996 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6327 (m-30) REVERT: B 40 GLU cc_start: 0.6054 (OUTLIER) cc_final: 0.4839 (tp30) REVERT: B 43 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6574 (tmm160) REVERT: B 280 ASP cc_start: 0.6051 (p0) cc_final: 0.5753 (p0) REVERT: B 492 ASP cc_start: 0.6594 (p0) cc_final: 0.6306 (p0) REVERT: B 572 ASP cc_start: 0.6432 (OUTLIER) cc_final: 0.6183 (m-30) REVERT: B 684 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: B 702 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7343 (mp-120) REVERT: B 719 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: C 280 ASP cc_start: 0.5995 (p0) cc_final: 0.5663 (p0) REVERT: C 323 ILE cc_start: 0.7905 (mp) cc_final: 0.7568 (mt) REVERT: C 492 ASP cc_start: 0.6610 (p0) cc_final: 0.6341 (p0) REVERT: C 572 ASP cc_start: 0.6423 (OUTLIER) cc_final: 0.6147 (m-30) REVERT: C 684 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7051 (mt-10) REVERT: C 702 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7340 (mp-120) REVERT: C 719 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: C 996 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6281 (m-30) REVERT: D 280 ASP cc_start: 0.5990 (p0) cc_final: 0.5743 (p0) REVERT: D 323 ILE cc_start: 0.7926 (mp) cc_final: 0.7584 (mt) REVERT: D 492 ASP cc_start: 0.6601 (p0) cc_final: 0.6318 (p0) REVERT: D 572 ASP cc_start: 0.6433 (OUTLIER) cc_final: 0.6160 (m-30) REVERT: D 684 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: D 702 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7360 (mp-120) REVERT: D 719 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: D 996 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6302 (m-30) REVERT: D 1020 TRP cc_start: 0.8036 (OUTLIER) cc_final: 0.7316 (t60) outliers start: 252 outliers final: 192 residues processed: 532 average time/residue: 0.4360 time to fit residues: 378.5040 Evaluate side-chains 515 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 300 time to evaluate : 3.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 804 ASN Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 ASN Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 719 GLN Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 914 CYS Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 719 GLN Chi-restraints excluded: chain D residue 743 SER Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 914 CYS Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 309 optimal weight: 0.5980 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 33792 Z= 0.260 Angle : 0.608 11.643 46104 Z= 0.316 Chirality : 0.044 0.223 4820 Planarity : 0.004 0.042 6088 Dihedral : 5.774 59.844 4512 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 7.15 % Allowed : 22.45 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: 0.05 (0.13), residues: 4080 helix: 0.04 (0.23), residues: 564 sheet: 0.72 (0.13), residues: 1412 loop : -0.39 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 553 HIS 0.003 0.001 HIS D 391 PHE 0.015 0.002 PHE C 209 TYR 0.010 0.002 TYR B1014 ARG 0.004 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 307 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6605 (tmm160) REVERT: A 135 GLN cc_start: 0.7352 (tt0) cc_final: 0.7146 (tt0) REVERT: A 237 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7654 (ttp-110) REVERT: A 280 ASP cc_start: 0.5997 (p0) cc_final: 0.5702 (p0) REVERT: A 492 ASP cc_start: 0.6609 (p0) cc_final: 0.6331 (p0) REVERT: A 572 ASP cc_start: 0.6374 (OUTLIER) cc_final: 0.6137 (m-30) REVERT: A 684 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: A 702 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7390 (mp-120) REVERT: A 719 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: B 237 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7724 (ttp-110) REVERT: B 249 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6884 (pp20) REVERT: B 280 ASP cc_start: 0.6011 (p0) cc_final: 0.5713 (p0) REVERT: B 492 ASP cc_start: 0.6587 (p0) cc_final: 0.6308 (p0) REVERT: B 572 ASP cc_start: 0.6389 (OUTLIER) cc_final: 0.6157 (m-30) REVERT: B 684 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6984 (mt-10) REVERT: B 702 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7396 (mp-120) REVERT: B 719 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: B 996 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.6261 (m-30) REVERT: C 135 GLN cc_start: 0.7348 (tt0) cc_final: 0.7133 (tt0) REVERT: C 280 ASP cc_start: 0.5953 (p0) cc_final: 0.5683 (p0) REVERT: C 323 ILE cc_start: 0.7911 (mp) cc_final: 0.7605 (mt) REVERT: C 492 ASP cc_start: 0.6603 (p0) cc_final: 0.6332 (p0) REVERT: C 572 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.6137 (m-30) REVERT: C 684 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: C 702 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7378 (mp-120) REVERT: D 135 GLN cc_start: 0.7352 (tt0) cc_final: 0.7137 (tt0) REVERT: D 280 ASP cc_start: 0.6026 (p0) cc_final: 0.5737 (p0) REVERT: D 323 ILE cc_start: 0.7912 (mp) cc_final: 0.7602 (mt) REVERT: D 492 ASP cc_start: 0.6595 (p0) cc_final: 0.6300 (p0) REVERT: D 572 ASP cc_start: 0.6398 (OUTLIER) cc_final: 0.6141 (m-30) REVERT: D 684 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: D 702 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7370 (mp-120) outliers start: 250 outliers final: 200 residues processed: 508 average time/residue: 0.4221 time to fit residues: 351.5612 Evaluate side-chains 513 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 295 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 743 SER Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 772 ASP Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 914 CYS Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 719 GLN Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 743 SER Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 914 CYS Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 581 ASN Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 655 MET Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 476 LYS Chi-restraints excluded: chain D residue 493 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 581 ASN Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 655 MET Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 739 HIS Chi-restraints excluded: chain D residue 743 SER Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.9980 chunk 376 optimal weight: 9.9990 chunk 343 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 287 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 5.9990 chunk 346 optimal weight: 3.9990 chunk 365 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33792 Z= 0.197 Angle : 0.594 11.346 46104 Z= 0.306 Chirality : 0.044 0.277 4820 Planarity : 0.004 0.040 6088 Dihedral : 5.552 59.928 4510 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.78 % Allowed : 24.06 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: 0.12 (0.13), residues: 4080 helix: 0.11 (0.23), residues: 560 sheet: 0.81 (0.14), residues: 1384 loop : -0.37 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 553 HIS 0.003 0.001 HIS B 391 PHE 0.015 0.001 PHE A 747 TYR 0.010 0.001 TYR C1014 ARG 0.003 0.000 ARG C 894 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 307 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6536 (tmm160) REVERT: A 280 ASP cc_start: 0.5940 (p0) cc_final: 0.5632 (p0) REVERT: A 492 ASP cc_start: 0.6527 (p0) cc_final: 0.6252 (p0) REVERT: A 572 ASP cc_start: 0.6317 (OUTLIER) cc_final: 0.6093 (m-30) REVERT: A 684 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6964 (mt-10) REVERT: A 702 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7426 (mp-120) REVERT: A 996 ASP cc_start: 0.6725 (OUTLIER) cc_final: 0.6288 (m-30) REVERT: B 135 GLN cc_start: 0.7524 (tm-30) cc_final: 0.7252 (tm-30) REVERT: B 237 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7642 (ttp-110) REVERT: B 280 ASP cc_start: 0.5955 (p0) cc_final: 0.5641 (p0) REVERT: B 492 ASP cc_start: 0.6514 (p0) cc_final: 0.6226 (p0) REVERT: B 572 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.6108 (m-30) REVERT: B 684 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6970 (mt-10) REVERT: B 702 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7430 (mp-120) REVERT: B 996 ASP cc_start: 0.6671 (OUTLIER) cc_final: 0.6253 (m-30) REVERT: C 280 ASP cc_start: 0.5941 (p0) cc_final: 0.5610 (p0) REVERT: C 323 ILE cc_start: 0.7875 (mp) cc_final: 0.7592 (mt) REVERT: C 572 ASP cc_start: 0.6337 (OUTLIER) cc_final: 0.6124 (m-30) REVERT: C 684 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6986 (mt-10) REVERT: C 702 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7426 (mp-120) REVERT: C 996 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.6271 (m-30) REVERT: D 280 ASP cc_start: 0.5895 (p0) cc_final: 0.5588 (p0) REVERT: D 323 ILE cc_start: 0.7874 (mp) cc_final: 0.7586 (mt) REVERT: D 572 ASP cc_start: 0.6343 (OUTLIER) cc_final: 0.6123 (m-30) REVERT: D 684 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: D 702 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7431 (mp-120) REVERT: D 1020 TRP cc_start: 0.8005 (OUTLIER) cc_final: 0.7372 (t60) outliers start: 202 outliers final: 158 residues processed: 471 average time/residue: 0.4180 time to fit residues: 328.3016 Evaluate side-chains 457 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 281 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 655 MET Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 894 ARG Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 655 MET Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 772 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 894 ARG Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.0670 chunk 387 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 406 optimal weight: 7.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33792 Z= 0.288 Angle : 0.628 11.647 46104 Z= 0.326 Chirality : 0.045 0.239 4820 Planarity : 0.004 0.042 6088 Dihedral : 5.705 59.421 4510 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.75 % Allowed : 24.14 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: 0.02 (0.13), residues: 4080 helix: 0.04 (0.23), residues: 556 sheet: 0.69 (0.13), residues: 1388 loop : -0.39 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 553 HIS 0.004 0.001 HIS C 363 PHE 0.016 0.002 PHE B 747 TYR 0.010 0.002 TYR B 856 ARG 0.005 0.000 ARG D 894 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 294 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6580 (tmm160) REVERT: A 280 ASP cc_start: 0.5988 (p0) cc_final: 0.5695 (p0) REVERT: A 492 ASP cc_start: 0.6667 (p0) cc_final: 0.6381 (p0) REVERT: A 572 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.6196 (m-30) REVERT: A 684 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: A 702 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7383 (mp-120) REVERT: A 996 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6298 (m-30) REVERT: A 1020 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7345 (t60) REVERT: B 135 GLN cc_start: 0.7494 (tm-30) cc_final: 0.7177 (tm-30) REVERT: B 237 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7753 (ttp-110) REVERT: B 280 ASP cc_start: 0.6009 (p0) cc_final: 0.5710 (p0) REVERT: B 492 ASP cc_start: 0.6643 (p0) cc_final: 0.6351 (p0) REVERT: B 572 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.6169 (m-30) REVERT: B 684 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: B 702 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7391 (mp-120) REVERT: B 996 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6286 (m-30) REVERT: B 1020 TRP cc_start: 0.8054 (OUTLIER) cc_final: 0.7338 (t60) REVERT: C 43 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6527 (tmm160) REVERT: C 280 ASP cc_start: 0.5996 (p0) cc_final: 0.5662 (p0) REVERT: C 323 ILE cc_start: 0.7928 (mp) cc_final: 0.7628 (mt) REVERT: C 542 MET cc_start: 0.6930 (ttp) cc_final: 0.6669 (ptt) REVERT: C 572 ASP cc_start: 0.6477 (OUTLIER) cc_final: 0.6224 (m-30) REVERT: C 684 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6989 (mt-10) REVERT: C 702 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7379 (mp-120) REVERT: C 996 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6310 (m-30) REVERT: C 1020 TRP cc_start: 0.8051 (OUTLIER) cc_final: 0.7358 (t60) REVERT: D 43 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.6552 (tmm160) REVERT: D 280 ASP cc_start: 0.5969 (p0) cc_final: 0.5663 (p0) REVERT: D 323 ILE cc_start: 0.7913 (mp) cc_final: 0.7613 (mt) REVERT: D 542 MET cc_start: 0.6920 (ttp) cc_final: 0.6666 (ptt) REVERT: D 572 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6229 (m-30) REVERT: D 684 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: D 702 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7383 (mp-120) REVERT: D 996 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6309 (m-30) REVERT: D 1020 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.7335 (t60) outliers start: 201 outliers final: 155 residues processed: 463 average time/residue: 0.4322 time to fit residues: 337.6984 Evaluate side-chains 468 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 289 time to evaluate : 3.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 MET Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 13 ARG Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 36 TRP Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 209 PHE Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 509 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain A residue 684 GLU Chi-restraints excluded: chain A residue 702 GLN Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 837 THR Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 997 ASP Chi-restraints excluded: chain A residue 999 TRP Chi-restraints excluded: chain A residue 1020 TRP Chi-restraints excluded: chain B residue 2 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 TRP Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 209 PHE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 655 MET Chi-restraints excluded: chain B residue 684 GLU Chi-restraints excluded: chain B residue 702 GLN Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 739 HIS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 837 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 963 SER Chi-restraints excluded: chain B residue 980 GLU Chi-restraints excluded: chain B residue 987 ASP Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 997 ASP Chi-restraints excluded: chain B residue 999 TRP Chi-restraints excluded: chain B residue 1020 TRP Chi-restraints excluded: chain C residue 2 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 33 PHE Chi-restraints excluded: chain C residue 36 TRP Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 374 GLN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 426 LEU Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 655 MET Chi-restraints excluded: chain C residue 684 GLU Chi-restraints excluded: chain C residue 702 GLN Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 739 HIS Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 765 LEU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 837 THR Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 869 ASP Chi-restraints excluded: chain C residue 963 SER Chi-restraints excluded: chain C residue 980 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 987 ASP Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 999 TRP Chi-restraints excluded: chain C residue 1020 TRP Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 33 PHE Chi-restraints excluded: chain D residue 36 TRP Chi-restraints excluded: chain D residue 43 ARG 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 124 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 209 PHE Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 374 GLN Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 509 ASP Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain D residue 702 GLN Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 795 VAL Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 869 ASP Chi-restraints excluded: chain D residue 963 SER Chi-restraints excluded: chain D residue 980 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 987 ASP Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 997 ASP Chi-restraints excluded: chain D residue 999 TRP Chi-restraints excluded: chain D residue 1020 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 324 optimal weight: 5.9990 chunk 135 optimal weight: 10.0000 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.090683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.075211 restraints weight = 67276.771| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.68 r_work: 0.2960 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 33792 Z= 0.320 Angle : 0.637 11.801 46104 Z= 0.331 Chirality : 0.045 0.224 4820 Planarity : 0.004 0.043 6088 Dihedral : 5.775 58.806 4510 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 5.66 % Allowed : 24.60 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 1.15 % 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: -0.11 (0.13), residues: 4080 helix: -0.07 (0.23), residues: 556 sheet: 0.59 (0.13), residues: 1404 loop : -0.48 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 553 HIS 0.004 0.001 HIS B 391 PHE 0.017 0.002 PHE D 747 TYR 0.010 0.002 TYR B 856 ARG 0.009 0.001 ARG C 894 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8460.67 seconds wall clock time: 152 minutes 9.32 seconds (9129.32 seconds total)