Starting phenix.real_space_refine on Fri Dec 15 22:07:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/12_2023/3j7h_5995.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/12_2023/3j7h_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_5995/12_2023/3j7h_5995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/12_2023/3j7h_5995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/12_2023/3j7h_5995.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7h_5995/12_2023/3j7h_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 16.97, 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: 14.10 Conformation dependent library (CDL) restraints added in 5.7 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: 4.90 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: 14.48 Time building geometry restraints manager: 14.58 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 10.080 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 89.250 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.230 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.580 ------------------------------------------------------------------------------- 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 : 3.631 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 outliers start: 428 outliers final: 206 residues processed: 1150 average time/residue: 0.5231 time to fit residues: 916.4468 Evaluate side-chains 622 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 416 time to evaluate : 3.637 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 206 outliers final: 8 residues processed: 206 average time/residue: 0.4266 time to fit residues: 148.4381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 2.9990 chunk 309 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 238 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 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 18 ASN A 30 HIS A 50 GLN ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS A 163 GLN A 226 HIS A 245 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 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 226 HIS B 245 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 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 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 226 HIS C 245 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 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 226 HIS D 245 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 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** D1022 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4112 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= 0.384 Angle : 0.778 13.461 46104 Z= 0.416 Chirality : 0.049 0.188 4820 Planarity : 0.008 0.065 6088 Dihedral : 5.998 21.608 4472 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.92 % Allowed : 19.82 % Favored : 74.26 % 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: 1.24 (0.13), residues: 4080 helix: 0.83 (0.21), residues: 556 sheet: 2.39 (0.14), residues: 1264 loop : -0.10 (0.12), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 769 HIS 0.016 0.002 HIS B 30 PHE 0.028 0.003 PHE B 209 TYR 0.021 0.002 TYR C 503 ARG 0.008 0.001 ARG A 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 638 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 431 time to evaluate : 3.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 207 outliers final: 108 residues processed: 584 average time/residue: 0.4592 time to fit residues: 434.4453 Evaluate side-chains 433 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 325 time to evaluate : 4.084 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 0 residues processed: 108 average time/residue: 0.3464 time to fit residues: 72.6294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 4.9990 chunk 400 optimal weight: 0.7980 chunk 330 optimal weight: 20.0000 chunk 368 optimal weight: 8.9990 chunk 126 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 ** 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 ** 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 ** 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** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 33792 Z= 0.376 Angle : 0.697 11.984 46104 Z= 0.366 Chirality : 0.047 0.184 4820 Planarity : 0.006 0.056 6088 Dihedral : 5.587 20.895 4472 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.63 % Allowed : 20.97 % Favored : 74.40 % 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: 0.82 (0.13), residues: 4080 helix: 0.46 (0.22), residues: 556 sheet: 1.66 (0.13), residues: 1392 loop : -0.17 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1020 HIS 0.006 0.002 HIS A 653 PHE 0.021 0.002 PHE B 33 TYR 0.017 0.002 TYR D 105 ARG 0.008 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 514 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 352 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 60 residues processed: 484 average time/residue: 0.4794 time to fit residues: 374.3964 Evaluate side-chains 358 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 298 time to evaluate : 6.522 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.3617 time to fit residues: 43.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 6.9990 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 9.9990 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 353 optimal weight: 3.9990 chunk 106 optimal weight: 0.0970 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 GLN A 646 HIS ** A 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 863 GLN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN B 646 HIS ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 GLN B 863 GLN ** 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 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 GLN C 625 GLN C 646 HIS ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 824 GLN C 863 GLN ** 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 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 GLN ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 824 GLN D 863 GLN ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 33792 Z= 0.325 Angle : 0.658 12.225 46104 Z= 0.344 Chirality : 0.045 0.192 4820 Planarity : 0.005 0.048 6088 Dihedral : 5.298 20.530 4472 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.18 % Allowed : 22.28 % Favored : 74.54 % 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: 0.42 (0.13), residues: 4080 helix: -0.02 (0.22), residues: 604 sheet: 1.23 (0.14), residues: 1412 loop : -0.26 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 553 HIS 0.005 0.001 HIS D1015 PHE 0.020 0.002 PHE C 747 TYR 0.013 0.002 TYR C1014 ARG 0.008 0.001 ARG D 894 *********************** 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 452 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 341 time to evaluate : 3.783 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 66 residues processed: 425 average time/residue: 0.4412 time to fit residues: 310.6611 Evaluate side-chains 369 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 303 time to evaluate : 4.119 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.3756 time to fit residues: 48.2880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 5 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 272 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 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** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 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 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 863 GLN ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 33792 Z= 0.353 Angle : 0.657 12.117 46104 Z= 0.343 Chirality : 0.046 0.223 4820 Planarity : 0.005 0.048 6088 Dihedral : 5.248 21.956 4472 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.29 % Allowed : 21.97 % Favored : 74.74 % 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: 0.21 (0.13), residues: 4080 helix: 0.02 (0.22), residues: 580 sheet: 0.95 (0.14), residues: 1412 loop : -0.34 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 553 HIS 0.004 0.001 HIS D 391 PHE 0.026 0.002 PHE A1007 TYR 0.012 0.002 TYR C 399 ARG 0.004 0.001 ARG C 442 *********************** 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 444 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 329 time to evaluate : 4.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 66 residues processed: 421 average time/residue: 0.4236 time to fit residues: 301.0565 Evaluate side-chains 352 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 286 time to evaluate : 3.734 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.3282 time to fit residues: 45.1258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 8.9990 chunk 355 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 0.0070 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 9.9990 chunk 327 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 761 GLN A 863 GLN ** A 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 GLN ** B 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** C 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 HIS D 863 GLN ** D 890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33792 Z= 0.283 Angle : 0.625 11.871 46104 Z= 0.326 Chirality : 0.044 0.205 4820 Planarity : 0.004 0.045 6088 Dihedral : 5.074 21.786 4472 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.83 % Allowed : 23.48 % Favored : 74.69 % 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: 0.09 (0.13), residues: 4080 helix: 0.01 (0.22), residues: 580 sheet: 0.83 (0.14), residues: 1408 loop : -0.40 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 553 HIS 0.005 0.001 HIS D 540 PHE 0.019 0.002 PHE D 33 TYR 0.011 0.002 TYR A1014 ARG 0.005 0.001 ARG C 442 *********************** 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 373 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 309 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 20 residues processed: 358 average time/residue: 0.4306 time to fit residues: 261.6452 Evaluate side-chains 291 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 3.938 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3036 time to fit residues: 16.5275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 224 optimal weight: 9.9990 chunk 288 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 332 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 393 optimal weight: 0.1980 chunk 246 optimal weight: 0.7980 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 GLN B 363 HIS B 863 GLN C 363 HIS C 863 GLN D 863 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 33792 Z= 0.188 Angle : 0.596 10.530 46104 Z= 0.307 Chirality : 0.043 0.180 4820 Planarity : 0.004 0.041 6088 Dihedral : 4.775 21.500 4472 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.57 % Allowed : 23.08 % Favored : 75.34 % 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: 0.21 (0.13), residues: 4080 helix: 0.10 (0.23), residues: 580 sheet: 0.89 (0.14), residues: 1380 loop : -0.29 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 553 HIS 0.003 0.001 HIS D 540 PHE 0.015 0.001 PHE D 747 TYR 0.011 0.001 TYR B1014 ARG 0.004 0.000 ARG A 442 *********************** 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 385 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 330 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 33 residues processed: 357 average time/residue: 0.4436 time to fit residues: 266.8891 Evaluate side-chains 324 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 291 time to evaluate : 3.656 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3334 time to fit residues: 25.0150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.0870 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 250 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 3.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS B 363 HIS B 573 GLN B 863 GLN ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 HIS C 363 HIS C 573 GLN C 863 GLN D 357 HIS D 363 HIS D 573 GLN D 863 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33792 Z= 0.226 Angle : 0.612 11.686 46104 Z= 0.314 Chirality : 0.043 0.207 4820 Planarity : 0.004 0.040 6088 Dihedral : 4.791 21.672 4472 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.74 % Allowed : 24.54 % Favored : 74.71 % 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: 0.18 (0.13), residues: 4080 helix: 0.07 (0.23), residues: 580 sheet: 0.86 (0.14), residues: 1380 loop : -0.31 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 553 HIS 0.003 0.001 HIS C 540 PHE 0.022 0.001 PHE B1007 TYR 0.010 0.001 TYR D1014 ARG 0.003 0.000 ARG D 699 *********************** 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 335 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 309 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 327 average time/residue: 0.4257 time to fit residues: 237.0017 Evaluate side-chains 292 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 281 time to evaluate : 3.751 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3348 time to fit residues: 11.9411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 5.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 331 optimal weight: 10.0000 chunk 346 optimal weight: 0.9980 chunk 365 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS A 573 GLN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 HIS ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 HIS ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 GLN C 863 GLN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 HIS ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 33792 Z= 0.335 Angle : 0.650 11.226 46104 Z= 0.334 Chirality : 0.045 0.219 4820 Planarity : 0.004 0.042 6088 Dihedral : 5.028 21.908 4472 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.03 % Allowed : 24.97 % Favored : 74.00 % 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: 0.01 (0.13), residues: 4080 helix: 0.11 (0.23), residues: 556 sheet: 0.73 (0.13), residues: 1384 loop : -0.46 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 90 HIS 0.005 0.001 HIS A1015 PHE 0.017 0.002 PHE A 33 TYR 0.012 0.002 TYR D 503 ARG 0.004 0.001 ARG C 37 *********************** 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 325 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 289 time to evaluate : 3.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 317 average time/residue: 0.4342 time to fit residues: 234.9409 Evaluate side-chains 287 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 267 time to evaluate : 4.024 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3351 time to fit residues: 17.6717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 406 optimal weight: 0.0050 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 250 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 HIS ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 863 GLN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33792 Z= 0.248 Angle : 0.630 12.144 46104 Z= 0.321 Chirality : 0.044 0.235 4820 Planarity : 0.004 0.040 6088 Dihedral : 4.896 22.085 4472 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.20 % Allowed : 25.46 % Favored : 74.34 % 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: -0.03 (0.13), residues: 4080 helix: 0.03 (0.23), residues: 560 sheet: 0.69 (0.13), residues: 1380 loop : -0.46 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 553 HIS 0.003 0.001 HIS B1015 PHE 0.016 0.001 PHE C 747 TYR 0.011 0.001 TYR D1014 ARG 0.003 0.000 ARG D 26 ********************** 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 308 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 301 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 305 average time/residue: 0.4439 time to fit residues: 230.4753 Evaluate side-chains 267 residues out of total 3496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 264 time to evaluate : 3.962 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3625 time to fit residues: 7.3159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 950 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 = 0.3359 r_free = 0.3359 target = 0.090730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075637 restraints weight = 67365.345| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.63 r_work: 0.2969 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 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 : 0.006 0.041 33792 Z= 0.420 Angle : 0.699 12.390 46104 Z= 0.360 Chirality : 0.046 0.237 4820 Planarity : 0.005 0.044 6088 Dihedral : 5.206 22.000 4472 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.80 % Allowed : 25.57 % Favored : 73.63 % 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: -0.35 (0.13), residues: 4080 helix: -0.33 (0.22), residues: 580 sheet: 0.49 (0.13), residues: 1400 loop : -0.66 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 90 HIS 0.006 0.001 HIS C 540 PHE 0.019 0.002 PHE D1007 TYR 0.012 0.002 TYR C 503 ARG 0.005 0.001 ARG D 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7872.92 seconds wall clock time: 143 minutes 11.88 seconds (8591.88 seconds total)