Starting phenix.real_space_refine on Sun Sep 29 13:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/09_2024/6hjp_0235.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/09_2024/6hjp_0235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/09_2024/6hjp_0235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/09_2024/6hjp_0235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/09_2024/6hjp_0235.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/09_2024/6hjp_0235.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 13878 2.51 5 N 3690 2.21 5 O 4476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 22134 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "B" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "C" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "D" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "E" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "F" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "H" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "I" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "J" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "L" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 13.96, per 1000 atoms: 0.63 Number of scatterers: 22134 At special positions: 0 Unit cell: (178.948, 164.934, 174.636, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 4476 8.00 N 3690 7.00 C 13878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.01 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.01 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 137 " distance=2.05 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.01 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 199 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 199 " distance=2.05 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.05 Simple disulfide: pdb=" SG CYS K 143 " - pdb=" SG CYS K 199 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " BETA1-6 " NAG N 1 " - " FUC N 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 4 " " NAG X 1 " - " FUC X 4 " NAG-ASN " NAG M 1 " - " ASN A 15 " " NAG N 1 " - " ASN A 27 " " NAG O 1 " - " ASN A 91 " " NAG P 1 " - " ASN A 290 " " NAG Q 1 " - " ASN B 154 " " NAG R 1 " - " ASN C 15 " " NAG S 1 " - " ASN C 27 " " NAG T 1 " - " ASN C 91 " " NAG U 1 " - " ASN C 290 " " NAG V 1 " - " ASN D 154 " " NAG W 1 " - " ASN E 15 " " NAG X 1 " - " ASN E 27 " " NAG Y 1 " - " ASN E 91 " " NAG Z 1 " - " ASN E 290 " " NAG a 1 " - " ASN F 154 " Time building additional restraints: 5.78 Conformation dependent library (CDL) restraints added in 2.7 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 63 sheets defined 18.1% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.817A pdb=" N LEU A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR A 76 " --> pdb=" O LEU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.511A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 125 removed outlier: 3.954A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.548A pdb=" N GLY B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.708A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 67 Processing helix chain 'C' and resid 72 through 76 removed outlier: 3.817A pdb=" N LEU C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR C 76 " --> pdb=" O LEU C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 76' Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 37 through 59 removed outlier: 3.510A pdb=" N THR D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 125 removed outlier: 3.955A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.549A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 161 Processing helix chain 'D' and resid 162 through 174 removed outlier: 3.707A pdb=" N LYS D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 72 through 76 removed outlier: 3.817A pdb=" N LEU E 75 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR E 76 " --> pdb=" O LEU E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 72 through 76' Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'F' and resid 37 through 59 removed outlier: 3.512A pdb=" N THR F 41 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN F 42 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 125 removed outlier: 3.954A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 removed outlier: 3.548A pdb=" N GLY F 155 " --> pdb=" O SER F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 161 Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.707A pdb=" N LYS F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.559A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.787A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.640A pdb=" N ASP G 90 " --> pdb=" O ARG G 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 91' Processing helix chain 'H' and resid 122 through 129 removed outlier: 3.964A pdb=" N LEU H 126 " --> pdb=" O SER H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 4.152A pdb=" N TYR H 187 " --> pdb=" O SER H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.556A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.785A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.639A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.553A pdb=" N SER K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.785A pdb=" N LYS K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.641A pdb=" N ASP K 90 " --> pdb=" O ARG K 87 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR K 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 87 through 91' Processing helix chain 'J' and resid 122 through 129 removed outlier: 3.965A pdb=" N LEU J 126 " --> pdb=" O SER J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 4.152A pdb=" N TYR J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.964A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 4.153A pdb=" N TYR L 187 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.173A pdb=" N SER A 48 " --> pdb=" O THR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 57 removed outlier: 6.720A pdb=" N LEU A 54 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 97 through 99 removed outlier: 3.711A pdb=" N PHE A 258 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 97 through 99 removed outlier: 8.008A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AA9, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB1, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AB2, first strand: chain 'C' and resid 7 through 11 Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB5, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.173A pdb=" N SER C 48 " --> pdb=" O THR C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 54 through 57 removed outlier: 6.720A pdb=" N LEU C 54 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 97 through 99 removed outlier: 3.712A pdb=" N PHE C 258 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 97 through 99 removed outlier: 8.006A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC1, first strand: chain 'C' and resid 287 through 288 Processing sheet with id=AC2, first strand: chain 'C' and resid 295 through 296 Processing sheet with id=AC3, first strand: chain 'E' and resid 7 through 11 Processing sheet with id=AC4, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AC5, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AC6, first strand: chain 'E' and resid 48 through 49 removed outlier: 6.173A pdb=" N SER E 48 " --> pdb=" O THR E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 54 through 57 removed outlier: 6.721A pdb=" N LEU E 54 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 97 through 99 removed outlier: 3.711A pdb=" N PHE E 258 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 97 through 99 removed outlier: 8.007A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AD3, first strand: chain 'E' and resid 295 through 296 Processing sheet with id=AD4, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.868A pdb=" N THR G 119 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.868A pdb=" N THR G 119 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU G 178 " --> pdb=" O GLN G 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 153 through 157 Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 67 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.807A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.807A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR H 98 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 115 through 119 removed outlier: 5.312A pdb=" N SER H 132 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU H 182 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL H 134 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU H 180 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU H 136 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER H 178 " --> pdb=" O LEU H 136 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN H 138 " --> pdb=" O LEU H 176 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU H 176 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 145 through 151 Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.863A pdb=" N THR I 119 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.863A pdb=" N THR I 119 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE I 111 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU I 178 " --> pdb=" O GLN I 174 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 153 through 157 Processing sheet with id=AF3, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.865A pdb=" N THR K 119 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.865A pdb=" N THR K 119 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE K 111 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR K 179 " --> pdb=" O ASP K 147 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR K 179 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU K 178 " --> pdb=" O GLN K 174 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 153 through 157 Processing sheet with id=AF9, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER J 67 " --> pdb=" O GLU J 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.807A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.807A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR J 98 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.312A pdb=" N SER J 132 " --> pdb=" O LEU J 182 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU J 182 " --> pdb=" O SER J 132 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL J 134 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU J 180 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU J 136 " --> pdb=" O SER J 178 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER J 178 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN J 138 " --> pdb=" O LEU J 176 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU J 176 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 145 through 151 Processing sheet with id=AG5, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.806A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.806A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.312A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 145 through 151 885 hydrogen bonds defined for protein. 2331 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: 8.43 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4368 1.32 - 1.45: 5889 1.45 - 1.57: 12246 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22623 Sorted by residual: bond pdb=" N GLU B 139 " pdb=" CA GLU B 139 " ideal model delta sigma weight residual 1.459 1.396 0.063 9.10e-03 1.21e+04 4.76e+01 bond pdb=" N GLU F 139 " pdb=" CA GLU F 139 " ideal model delta sigma weight residual 1.459 1.397 0.063 9.10e-03 1.21e+04 4.75e+01 bond pdb=" N GLU D 139 " pdb=" CA GLU D 139 " ideal model delta sigma weight residual 1.459 1.397 0.062 9.10e-03 1.21e+04 4.65e+01 bond pdb=" N HIS D 142 " pdb=" CA HIS D 142 " ideal model delta sigma weight residual 1.456 1.415 0.042 1.14e-02 7.69e+03 1.33e+01 bond pdb=" N HIS F 142 " pdb=" CA HIS F 142 " ideal model delta sigma weight residual 1.456 1.415 0.042 1.14e-02 7.69e+03 1.33e+01 ... (remaining 22618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 28288 2.03 - 4.05: 2168 4.05 - 6.08: 210 6.08 - 8.10: 48 8.10 - 10.13: 9 Bond angle restraints: 30723 Sorted by residual: angle pdb=" CA PHE F 140 " pdb=" CB PHE F 140 " pdb=" CG PHE F 140 " ideal model delta sigma weight residual 113.80 107.03 6.77 1.00e+00 1.00e+00 4.58e+01 angle pdb=" CA PHE D 140 " pdb=" CB PHE D 140 " pdb=" CG PHE D 140 " ideal model delta sigma weight residual 113.80 107.07 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" CA PHE B 140 " pdb=" CB PHE B 140 " pdb=" CG PHE B 140 " ideal model delta sigma weight residual 113.80 107.12 6.68 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C TYR B 141 " pdb=" CA TYR B 141 " pdb=" CB TYR B 141 " ideal model delta sigma weight residual 110.79 101.02 9.77 1.66e+00 3.63e-01 3.46e+01 angle pdb=" C TYR D 141 " pdb=" CA TYR D 141 " pdb=" CB TYR D 141 " ideal model delta sigma weight residual 110.79 101.18 9.61 1.66e+00 3.63e-01 3.35e+01 ... (remaining 30718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 13336 22.10 - 44.21: 578 44.21 - 66.31: 57 66.31 - 88.41: 72 88.41 - 110.52: 36 Dihedral angle restraints: 14079 sinusoidal: 6069 harmonic: 8010 Sorted by residual: dihedral pdb=" C ASP F 158 " pdb=" N ASP F 158 " pdb=" CA ASP F 158 " pdb=" CB ASP F 158 " ideal model delta harmonic sigma weight residual -122.60 -138.20 15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C ASP B 158 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " ideal model delta harmonic sigma weight residual -122.60 -137.92 15.32 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" C ASP D 158 " pdb=" N ASP D 158 " pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 14076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 3411 0.168 - 0.336: 108 0.336 - 0.504: 13 0.504 - 0.672: 2 0.672 - 0.840: 3 Chirality restraints: 3537 Sorted by residual: chirality pdb=" C1 MAN Y 4 " pdb=" O3 BMA Y 3 " pdb=" C2 MAN Y 4 " pdb=" O5 MAN Y 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.77e+03 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 1.57 0.83 2.00e-02 2.50e+03 1.73e+03 chirality pdb=" C1 MAN O 4 " pdb=" O3 BMA O 3 " pdb=" C2 MAN O 4 " pdb=" O5 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.40 1.59 0.81 2.00e-02 2.50e+03 1.65e+03 ... (remaining 3534 not shown) Planarity restraints: 3915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG N 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " -0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG S 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.338 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG X 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.117 2.00e-02 2.50e+03 ... (remaining 3912 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 972 2.71 - 3.25: 19736 3.25 - 3.80: 33860 3.80 - 4.35: 41404 4.35 - 4.90: 72331 Nonbonded interactions: 168303 Sorted by model distance: nonbonded pdb=" O3 NAG Y 1 " pdb=" O7 NAG Y 1 " model vdw 2.158 3.040 nonbonded pdb=" O3 NAG O 1 " pdb=" O7 NAG O 1 " model vdw 2.159 3.040 nonbonded pdb=" O3 NAG T 1 " pdb=" O7 NAG T 1 " model vdw 2.159 3.040 nonbonded pdb=" OG SER D 151 " pdb=" O THR D 156 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 151 " pdb=" O THR B 156 " model vdw 2.230 3.040 ... (remaining 168298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'Q' selection = chain 'V' selection = chain 'a' } 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: 9.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 51.490 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 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 : 0.008 0.063 22623 Z= 0.521 Angle : 1.170 10.130 30723 Z= 0.697 Chirality : 0.088 0.840 3537 Planarity : 0.018 0.292 3900 Dihedral : 14.764 110.517 8871 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.90 % Favored : 91.88 % Rotamer: Outliers : 2.40 % Allowed : 4.76 % Favored : 92.85 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 2760 helix: -0.78 (0.22), residues: 423 sheet: -0.57 (0.17), residues: 843 loop : -2.46 (0.13), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP E 153 HIS 0.009 0.002 HIS B 25 PHE 0.017 0.003 PHE G 149 TYR 0.023 0.003 TYR B 141 ARG 0.005 0.001 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 314 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 ARG cc_start: 0.8456 (ttm170) cc_final: 0.8222 (mtp180) REVERT: D 149 MET cc_start: 0.9299 (mmt) cc_final: 0.9027 (mmp) REVERT: F 129 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8303 (p0) REVERT: G 73 ASP cc_start: 0.8348 (t0) cc_final: 0.7743 (t0) REVERT: G 90 ASP cc_start: 0.9123 (m-30) cc_final: 0.8902 (m-30) REVERT: G 174 GLN cc_start: 0.7627 (pt0) cc_final: 0.7407 (pm20) REVERT: G 197 TYR cc_start: 0.6842 (m-80) cc_final: 0.6151 (m-80) REVERT: G 213 ARG cc_start: 0.7851 (ttt180) cc_final: 0.7313 (tmt-80) REVERT: H 4 MET cc_start: 0.8578 (mmm) cc_final: 0.8035 (mmm) REVERT: H 140 PHE cc_start: 0.8139 (p90) cc_final: 0.7696 (p90) REVERT: H 143 ARG cc_start: 0.8918 (tmt-80) cc_final: 0.8332 (tpt90) REVERT: H 166 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8928 (mp0) REVERT: H 168 ASP cc_start: 0.7560 (t70) cc_final: 0.7125 (t0) REVERT: I 6 GLU cc_start: 0.8476 (pt0) cc_final: 0.8205 (pt0) REVERT: I 73 ASP cc_start: 0.8150 (t0) cc_final: 0.7495 (t0) REVERT: I 89 ASP cc_start: 0.9399 (p0) cc_final: 0.9071 (p0) REVERT: I 146 LYS cc_start: 0.8398 (tttp) cc_final: 0.8079 (tptp) REVERT: I 147 ASP cc_start: 0.8601 (m-30) cc_final: 0.8179 (m-30) REVERT: I 211 ASP cc_start: 0.6683 (m-30) cc_final: 0.6185 (t70) REVERT: I 212 LYS cc_start: 0.4815 (tppt) cc_final: 0.4604 (tptt) REVERT: I 215 GLU cc_start: 0.5643 (pt0) cc_final: 0.5416 (tp30) REVERT: K 73 ASP cc_start: 0.8420 (t0) cc_final: 0.7947 (t0) REVERT: K 89 ASP cc_start: 0.9387 (p0) cc_final: 0.9059 (p0) REVERT: K 207 ASN cc_start: 0.8968 (m110) cc_final: 0.8645 (p0) REVERT: J 108 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8702 (tptt) REVERT: J 143 ARG cc_start: 0.8777 (tmt-80) cc_final: 0.8172 (tpt90) REVERT: L 24 ARG cc_start: 0.8539 (mtp-110) cc_final: 0.8265 (mtp-110) REVERT: L 108 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8407 (tptt) REVERT: L 140 PHE cc_start: 0.7780 (p90) cc_final: 0.7495 (p90) REVERT: L 143 ARG cc_start: 0.8676 (tmt-80) cc_final: 0.8417 (tmt-80) outliers start: 57 outliers final: 11 residues processed: 363 average time/residue: 0.4066 time to fit residues: 213.0849 Evaluate side-chains 173 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 129 ASN Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 129 ASN Chi-restraints excluded: chain G residue 141 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.9990 chunk 206 optimal weight: 0.3980 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 247 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 184 HIS A 196 GLN A 250 ASN A 299 HIS A 323 ASN B 169 ASN C 184 HIS C 250 ASN C 299 HIS C 323 ASN E 55 GLN E 184 HIS E 250 ASN E 299 HIS E 323 ASN G 200 ASN H 37 GLN H 156 GLN I 13 GLN K 114 GLN J 37 GLN J 167 GLN L 37 GLN L 139 ASN L 156 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22623 Z= 0.212 Angle : 0.715 14.372 30723 Z= 0.354 Chirality : 0.047 0.269 3537 Planarity : 0.005 0.056 3900 Dihedral : 12.404 85.974 4006 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.68 % Allowed : 9.26 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.15), residues: 2760 helix: 0.80 (0.25), residues: 423 sheet: -0.23 (0.17), residues: 909 loop : -2.03 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 255 HIS 0.004 0.001 HIS H 190 PHE 0.017 0.001 PHE I 68 TYR 0.015 0.001 TYR H 193 ARG 0.004 0.001 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 127 ARG cc_start: 0.8650 (mpt-90) cc_final: 0.8236 (mtm110) REVERT: D 149 MET cc_start: 0.9311 (mmt) cc_final: 0.8727 (mmt) REVERT: E 177 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9251 (tp) REVERT: E 230 MET cc_start: 0.8342 (mtp) cc_final: 0.8107 (mtp) REVERT: G 43 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8208 (mmtm) REVERT: G 73 ASP cc_start: 0.8306 (t0) cc_final: 0.7979 (t0) REVERT: G 90 ASP cc_start: 0.9064 (m-30) cc_final: 0.8842 (m-30) REVERT: G 114 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8325 (tp-100) REVERT: G 197 TYR cc_start: 0.6671 (m-80) cc_final: 0.6031 (m-80) REVERT: G 202 ASN cc_start: 0.7563 (t0) cc_final: 0.7171 (p0) REVERT: G 213 ARG cc_start: 0.7740 (ttt180) cc_final: 0.6917 (tmt-80) REVERT: H 4 MET cc_start: 0.8571 (mmm) cc_final: 0.8200 (mmm) REVERT: H 140 PHE cc_start: 0.7900 (p90) cc_final: 0.7574 (p90) REVERT: H 143 ARG cc_start: 0.8866 (tmt-80) cc_final: 0.8127 (tpt170) REVERT: H 166 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8923 (mp0) REVERT: I 73 ASP cc_start: 0.8215 (t0) cc_final: 0.7443 (t0) REVERT: I 76 LYS cc_start: 0.9290 (mtpp) cc_final: 0.9030 (mttm) REVERT: I 89 ASP cc_start: 0.9410 (p0) cc_final: 0.9083 (p0) REVERT: I 146 LYS cc_start: 0.8275 (tttp) cc_final: 0.7889 (tttp) REVERT: I 147 ASP cc_start: 0.8476 (m-30) cc_final: 0.8158 (m-30) REVERT: I 211 ASP cc_start: 0.6558 (m-30) cc_final: 0.6197 (t0) REVERT: I 212 LYS cc_start: 0.4998 (tppt) cc_final: 0.4680 (mmmt) REVERT: I 215 GLU cc_start: 0.5702 (pt0) cc_final: 0.5206 (tp30) REVERT: K 73 ASP cc_start: 0.8436 (t0) cc_final: 0.8054 (t0) REVERT: K 89 ASP cc_start: 0.9367 (p0) cc_final: 0.9087 (p0) REVERT: K 99 MET cc_start: 0.9195 (mmt) cc_final: 0.8919 (mmt) REVERT: J 108 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8592 (tptt) REVERT: J 143 ARG cc_start: 0.8550 (tmt-80) cc_final: 0.8156 (tpt90) REVERT: J 191 LYS cc_start: 0.7253 (ttmp) cc_final: 0.6832 (tmtt) REVERT: L 24 ARG cc_start: 0.8485 (mtp-110) cc_final: 0.7861 (mtp-110) REVERT: L 70 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8631 (mm-30) REVERT: L 106 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: L 108 LYS cc_start: 0.8931 (ttpt) cc_final: 0.8279 (tptt) REVERT: L 140 PHE cc_start: 0.7443 (p90) cc_final: 0.7112 (p90) REVERT: L 143 ARG cc_start: 0.8690 (tmt-80) cc_final: 0.8451 (tpt-90) outliers start: 40 outliers final: 18 residues processed: 210 average time/residue: 0.4404 time to fit residues: 134.4767 Evaluate side-chains 166 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 149 TRP Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 206 optimal weight: 0.0770 chunk 168 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 221 optimal weight: 4.9990 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 184 HIS C 12 HIS C 150 ASN C 184 HIS E 150 ASN E 184 HIS H 6 GLN H 156 GLN J 6 GLN J 167 GLN L 6 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 22623 Z= 0.512 Angle : 0.771 19.129 30723 Z= 0.392 Chirality : 0.050 0.205 3537 Planarity : 0.005 0.059 3900 Dihedral : 10.517 78.745 3996 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.16 % Allowed : 9.39 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 2760 helix: 1.01 (0.25), residues: 423 sheet: -0.06 (0.17), residues: 915 loop : -1.77 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 112 HIS 0.007 0.002 HIS A 184 PHE 0.031 0.003 PHE I 68 TYR 0.021 0.002 TYR C 102 ARG 0.023 0.001 ARG I 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 143 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9201 (mm) REVERT: C 184 HIS cc_start: 0.8487 (OUTLIER) cc_final: 0.7595 (p90) REVERT: G 73 ASP cc_start: 0.8231 (t0) cc_final: 0.7960 (t0) REVERT: G 114 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8404 (tp-100) REVERT: G 202 ASN cc_start: 0.7487 (t0) cc_final: 0.6965 (p0) REVERT: G 213 ARG cc_start: 0.7720 (ttt180) cc_final: 0.6802 (tmt-80) REVERT: H 4 MET cc_start: 0.8736 (mmm) cc_final: 0.8123 (mmm) REVERT: H 24 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8205 (mtp-110) REVERT: H 140 PHE cc_start: 0.7986 (p90) cc_final: 0.7543 (p90) REVERT: H 143 ARG cc_start: 0.8651 (tmt-80) cc_final: 0.8373 (tpt-90) REVERT: I 1 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7963 (tm-30) REVERT: I 73 ASP cc_start: 0.8312 (t0) cc_final: 0.7812 (t0) REVERT: I 146 LYS cc_start: 0.8169 (tttp) cc_final: 0.7760 (tttp) REVERT: I 147 ASP cc_start: 0.8494 (m-30) cc_final: 0.8151 (m-30) REVERT: I 211 ASP cc_start: 0.6825 (m-30) cc_final: 0.6336 (t0) REVERT: I 212 LYS cc_start: 0.4963 (tppt) cc_final: 0.4652 (mmmt) REVERT: K 73 ASP cc_start: 0.8367 (t0) cc_final: 0.8012 (t0) REVERT: K 99 MET cc_start: 0.9231 (mmt) cc_final: 0.8876 (mmt) REVERT: J 108 LYS cc_start: 0.9045 (ttpt) cc_final: 0.8604 (tptt) REVERT: L 106 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7721 (tm-30) REVERT: L 108 LYS cc_start: 0.8950 (ttpt) cc_final: 0.8295 (tptt) REVERT: L 140 PHE cc_start: 0.7737 (p90) cc_final: 0.7102 (p90) REVERT: L 143 ARG cc_start: 0.8624 (tmt-80) cc_final: 0.8349 (tpt-90) outliers start: 75 outliers final: 40 residues processed: 206 average time/residue: 0.4326 time to fit residues: 131.7447 Evaluate side-chains 176 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 296 GLN Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 5 LEU Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 184 LYS Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 106 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 128 optimal weight: 0.0570 chunk 27 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 166 optimal weight: 30.0000 chunk 249 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 chunk 130 optimal weight: 0.1980 chunk 236 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 HIS E 296 GLN G 114 GLN H 159 ASN I 158 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 22623 Z= 0.148 Angle : 0.633 21.075 30723 Z= 0.308 Chirality : 0.044 0.213 3537 Planarity : 0.004 0.052 3900 Dihedral : 9.220 69.961 3996 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.48 % Allowed : 10.40 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.16), residues: 2760 helix: 1.64 (0.26), residues: 423 sheet: 0.12 (0.17), residues: 951 loop : -1.46 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 149 HIS 0.011 0.001 HIS E 184 PHE 0.012 0.001 PHE K 68 TYR 0.012 0.001 TYR B 157 ARG 0.004 0.000 ARG F 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 150 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8327 (OUTLIER) cc_final: 0.7616 (p90) REVERT: E 49 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9087 (mm) REVERT: E 242 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.9001 (t) REVERT: G 73 ASP cc_start: 0.8187 (t0) cc_final: 0.7898 (t0) REVERT: G 114 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8341 (tp-100) REVERT: G 197 TYR cc_start: 0.6536 (m-80) cc_final: 0.6142 (m-80) REVERT: G 202 ASN cc_start: 0.7372 (t0) cc_final: 0.6733 (p0) REVERT: I 73 ASP cc_start: 0.8238 (t0) cc_final: 0.7737 (t0) REVERT: I 146 LYS cc_start: 0.8074 (tttp) cc_final: 0.7690 (tttp) REVERT: I 197 TYR cc_start: 0.7051 (m-80) cc_final: 0.6647 (m-80) REVERT: I 211 ASP cc_start: 0.6637 (m-30) cc_final: 0.6180 (t0) REVERT: I 212 LYS cc_start: 0.5024 (tppt) cc_final: 0.4658 (mmmt) REVERT: K 73 ASP cc_start: 0.8276 (t0) cc_final: 0.7974 (t0) REVERT: K 99 MET cc_start: 0.9142 (mmt) cc_final: 0.8916 (mmt) REVERT: J 108 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8634 (tptt) REVERT: J 109 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7173 (ptm-80) REVERT: L 108 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8361 (tptt) REVERT: L 140 PHE cc_start: 0.7614 (p90) cc_final: 0.6960 (p90) REVERT: L 143 ARG cc_start: 0.8616 (tmt-80) cc_final: 0.8299 (tpt-90) outliers start: 59 outliers final: 32 residues processed: 197 average time/residue: 0.4103 time to fit residues: 119.3300 Evaluate side-chains 169 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 109 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN B 128 ASN C 32 HIS C 184 HIS C 296 GLN E 296 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22623 Z= 0.301 Angle : 0.644 22.229 30723 Z= 0.315 Chirality : 0.045 0.224 3537 Planarity : 0.004 0.054 3900 Dihedral : 8.753 63.856 3992 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.44 % Allowed : 10.82 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2760 helix: 1.74 (0.26), residues: 423 sheet: 0.25 (0.17), residues: 939 loop : -1.37 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP J 149 HIS 0.006 0.001 HIS C 184 PHE 0.017 0.002 PHE C 115 TYR 0.012 0.001 TYR C 102 ARG 0.004 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 138 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.7688 (p90) REVERT: A 192 GLN cc_start: 0.9136 (tm-30) cc_final: 0.8872 (tm-30) REVERT: E 49 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9085 (mm) REVERT: E 242 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8997 (t) REVERT: G 43 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8193 (mmtm) REVERT: G 73 ASP cc_start: 0.8136 (t0) cc_final: 0.7861 (t0) REVERT: G 197 TYR cc_start: 0.6590 (m-80) cc_final: 0.5749 (m-80) REVERT: G 202 ASN cc_start: 0.7378 (t0) cc_final: 0.6706 (p0) REVERT: G 213 ARG cc_start: 0.7685 (ttt180) cc_final: 0.7086 (tmt-80) REVERT: I 73 ASP cc_start: 0.8260 (t0) cc_final: 0.7763 (t0) REVERT: I 146 LYS cc_start: 0.8134 (tttp) cc_final: 0.7736 (tttp) REVERT: I 197 TYR cc_start: 0.7037 (m-80) cc_final: 0.6658 (m-80) REVERT: I 211 ASP cc_start: 0.6682 (m-30) cc_final: 0.6197 (t0) REVERT: I 212 LYS cc_start: 0.5147 (tppt) cc_final: 0.4746 (mmmt) REVERT: K 73 ASP cc_start: 0.8229 (t0) cc_final: 0.7910 (t0) REVERT: K 99 MET cc_start: 0.9150 (mmt) cc_final: 0.8799 (mmt) REVERT: J 143 ARG cc_start: 0.8736 (tpt-90) cc_final: 0.8506 (tpt170) REVERT: L 106 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: L 108 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8336 (tptt) REVERT: L 140 PHE cc_start: 0.7634 (p90) cc_final: 0.6890 (p90) REVERT: L 143 ARG cc_start: 0.8547 (tmt-80) cc_final: 0.8193 (tpt-90) outliers start: 58 outliers final: 38 residues processed: 186 average time/residue: 0.4056 time to fit residues: 111.5018 Evaluate side-chains 172 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 6 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 148 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 264 optimal weight: 0.4980 chunk 219 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 231 ASN C 296 GLN D 128 ASN F 128 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22623 Z= 0.222 Angle : 0.619 22.929 30723 Z= 0.300 Chirality : 0.044 0.244 3537 Planarity : 0.004 0.050 3900 Dihedral : 8.278 59.943 3992 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.90 % Allowed : 10.69 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2760 helix: 1.97 (0.26), residues: 423 sheet: 0.40 (0.17), residues: 942 loop : -1.28 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 149 HIS 0.005 0.001 HIS C 184 PHE 0.014 0.001 PHE I 68 TYR 0.010 0.001 TYR B 157 ARG 0.003 0.000 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 137 time to evaluate : 2.571 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.7682 (p90) REVERT: A 192 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8866 (tm-30) REVERT: C 184 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7543 (p90) REVERT: E 49 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9077 (mm) REVERT: E 242 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8997 (t) REVERT: G 43 LYS cc_start: 0.8660 (mmtp) cc_final: 0.8232 (mmtm) REVERT: G 73 ASP cc_start: 0.8139 (t0) cc_final: 0.7830 (t0) REVERT: G 197 TYR cc_start: 0.6464 (m-80) cc_final: 0.6058 (m-80) REVERT: H 24 ARG cc_start: 0.8369 (mtp85) cc_final: 0.7495 (mtp85) REVERT: H 79 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6959 (mp10) REVERT: I 73 ASP cc_start: 0.8237 (t0) cc_final: 0.7590 (t0) REVERT: I 146 LYS cc_start: 0.8094 (tttp) cc_final: 0.7720 (tttp) REVERT: I 147 ASP cc_start: 0.8550 (m-30) cc_final: 0.8206 (m-30) REVERT: I 197 TYR cc_start: 0.7026 (m-80) cc_final: 0.6677 (m-80) REVERT: I 211 ASP cc_start: 0.6715 (m-30) cc_final: 0.6280 (t0) REVERT: K 73 ASP cc_start: 0.8152 (t0) cc_final: 0.7818 (t0) REVERT: K 99 MET cc_start: 0.9131 (mmt) cc_final: 0.8786 (mmt) REVERT: L 106 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: L 108 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8339 (tptt) outliers start: 69 outliers final: 43 residues processed: 194 average time/residue: 0.4136 time to fit residues: 118.6618 Evaluate side-chains 177 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 168 ASP Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 263 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 183 HIS A 296 GLN C 183 HIS C 296 GLN E 296 GLN L 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22623 Z= 0.354 Angle : 0.663 24.050 30723 Z= 0.326 Chirality : 0.046 0.231 3537 Planarity : 0.004 0.052 3900 Dihedral : 8.209 59.332 3992 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.90 % Allowed : 11.15 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2760 helix: 1.84 (0.26), residues: 423 sheet: 0.44 (0.17), residues: 933 loop : -1.28 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP J 149 HIS 0.006 0.002 HIS C 12 PHE 0.020 0.002 PHE C 115 TYR 0.015 0.002 TYR H 193 ARG 0.006 0.001 ARG L 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 123 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.7746 (p90) REVERT: A 192 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8890 (tm-30) REVERT: C 184 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.7590 (p90) REVERT: E 49 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9060 (mm) REVERT: E 242 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8980 (t) REVERT: G 43 LYS cc_start: 0.8759 (mmtp) cc_final: 0.8548 (mmtm) REVERT: G 73 ASP cc_start: 0.8157 (t0) cc_final: 0.7872 (t0) REVERT: G 197 TYR cc_start: 0.6518 (m-80) cc_final: 0.6099 (m-80) REVERT: H 24 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8122 (mtp-110) REVERT: H 79 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7190 (mp10) REVERT: H 143 ARG cc_start: 0.8666 (tpt-90) cc_final: 0.8459 (tmt-80) REVERT: I 73 ASP cc_start: 0.8274 (t0) cc_final: 0.7645 (t0) REVERT: I 146 LYS cc_start: 0.8110 (tttp) cc_final: 0.7725 (tttp) REVERT: I 197 TYR cc_start: 0.6989 (m-80) cc_final: 0.6628 (m-80) REVERT: I 211 ASP cc_start: 0.6912 (m-30) cc_final: 0.6484 (t0) REVERT: K 73 ASP cc_start: 0.8231 (t0) cc_final: 0.7890 (t0) REVERT: K 99 MET cc_start: 0.9162 (mmt) cc_final: 0.8774 (mmt) REVERT: L 106 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: L 108 LYS cc_start: 0.9029 (ttpt) cc_final: 0.8416 (tptt) outliers start: 69 outliers final: 46 residues processed: 182 average time/residue: 0.3827 time to fit residues: 103.8986 Evaluate side-chains 174 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 122 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 168 ASP Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 179 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN K 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22623 Z= 0.182 Angle : 0.603 23.273 30723 Z= 0.291 Chirality : 0.043 0.207 3537 Planarity : 0.004 0.051 3900 Dihedral : 7.751 59.937 3992 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.27 % Allowed : 11.83 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2760 helix: 2.12 (0.26), residues: 423 sheet: 0.63 (0.18), residues: 924 loop : -1.21 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP J 149 HIS 0.004 0.001 HIS K 203 PHE 0.011 0.001 PHE K 68 TYR 0.010 0.001 TYR H 193 ARG 0.006 0.000 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.7643 (p90) REVERT: A 192 GLN cc_start: 0.9131 (tm-30) cc_final: 0.8879 (tm-30) REVERT: E 242 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8990 (t) REVERT: G 43 LYS cc_start: 0.8725 (mmtp) cc_final: 0.8344 (mmtm) REVERT: G 73 ASP cc_start: 0.8125 (t0) cc_final: 0.7818 (t0) REVERT: G 197 TYR cc_start: 0.6311 (m-80) cc_final: 0.5950 (m-80) REVERT: H 24 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7470 (mtp85) REVERT: H 104 ARG cc_start: 0.8719 (ptm-80) cc_final: 0.8031 (ptt90) REVERT: I 73 ASP cc_start: 0.8284 (t0) cc_final: 0.7770 (t0) REVERT: I 146 LYS cc_start: 0.7995 (tttp) cc_final: 0.7708 (tttp) REVERT: I 197 TYR cc_start: 0.6926 (m-80) cc_final: 0.6569 (m-80) REVERT: I 211 ASP cc_start: 0.6798 (m-30) cc_final: 0.6388 (t0) REVERT: K 73 ASP cc_start: 0.8191 (t0) cc_final: 0.7869 (t0) REVERT: K 99 MET cc_start: 0.9130 (mmt) cc_final: 0.8779 (mmt) REVERT: K 126 LYS cc_start: 0.8354 (tptp) cc_final: 0.8028 (tptp) REVERT: L 106 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7528 (tm-30) REVERT: L 108 LYS cc_start: 0.9053 (ttpt) cc_final: 0.8465 (tptt) outliers start: 54 outliers final: 38 residues processed: 182 average time/residue: 0.3936 time to fit residues: 107.3982 Evaluate side-chains 170 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 129 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 0.6980 chunk 252 optimal weight: 4.9990 chunk 229 optimal weight: 0.1980 chunk 245 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 chunk 231 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN E 183 HIS E 296 GLN J 37 GLN L 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22623 Z= 0.249 Angle : 0.619 23.306 30723 Z= 0.301 Chirality : 0.044 0.200 3537 Planarity : 0.004 0.051 3900 Dihedral : 7.556 59.998 3992 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.31 % Allowed : 12.04 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2760 helix: 2.04 (0.26), residues: 426 sheet: 0.67 (0.18), residues: 924 loop : -1.21 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP J 149 HIS 0.004 0.001 HIS K 203 PHE 0.015 0.001 PHE C 115 TYR 0.014 0.001 TYR K 197 ARG 0.005 0.000 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 130 time to evaluate : 2.546 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8734 (OUTLIER) cc_final: 0.7747 (p90) REVERT: A 192 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8892 (tm-30) REVERT: C 184 HIS cc_start: 0.8575 (OUTLIER) cc_final: 0.7481 (p90) REVERT: E 242 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8979 (t) REVERT: G 43 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8388 (mmtm) REVERT: G 73 ASP cc_start: 0.8162 (t0) cc_final: 0.7801 (t0) REVERT: G 197 TYR cc_start: 0.6353 (m-80) cc_final: 0.6021 (m-80) REVERT: H 24 ARG cc_start: 0.8365 (mtp85) cc_final: 0.7459 (mtp85) REVERT: I 73 ASP cc_start: 0.8277 (t0) cc_final: 0.7786 (t0) REVERT: I 146 LYS cc_start: 0.8084 (tttp) cc_final: 0.7706 (tttp) REVERT: I 197 TYR cc_start: 0.6949 (m-80) cc_final: 0.6573 (m-80) REVERT: I 211 ASP cc_start: 0.6889 (m-30) cc_final: 0.6477 (t0) REVERT: K 73 ASP cc_start: 0.8176 (t0) cc_final: 0.7830 (t0) REVERT: K 99 MET cc_start: 0.9129 (mmt) cc_final: 0.8754 (mmt) REVERT: K 146 LYS cc_start: 0.7855 (tttp) cc_final: 0.7637 (tttp) REVERT: J 143 ARG cc_start: 0.8822 (tpt-90) cc_final: 0.8555 (tpt170) REVERT: L 106 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7535 (tm-30) REVERT: L 108 LYS cc_start: 0.9057 (ttpt) cc_final: 0.8460 (tptt) outliers start: 55 outliers final: 41 residues processed: 179 average time/residue: 0.3935 time to fit residues: 105.2167 Evaluate side-chains 170 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 125 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 2.9990 chunk 259 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 123 optimal weight: 0.0570 chunk 180 optimal weight: 0.0770 chunk 271 optimal weight: 3.9990 chunk 250 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.4262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN E 296 GLN J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22623 Z= 0.250 Angle : 0.616 23.466 30723 Z= 0.300 Chirality : 0.044 0.196 3537 Planarity : 0.004 0.055 3900 Dihedral : 7.476 59.948 3992 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.23 % Allowed : 12.12 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2760 helix: 2.03 (0.26), residues: 426 sheet: 0.69 (0.18), residues: 924 loop : -1.20 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J 149 HIS 0.004 0.001 HIS G 203 PHE 0.015 0.001 PHE C 115 TYR 0.013 0.001 TYR K 197 ARG 0.004 0.000 ARG I 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 128 time to evaluate : 2.449 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8753 (OUTLIER) cc_final: 0.7689 (p90) REVERT: A 192 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8909 (tm-30) REVERT: C 184 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.7423 (p90) REVERT: D 59 MET cc_start: 0.8514 (mmm) cc_final: 0.7816 (mmm) REVERT: E 242 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8980 (t) REVERT: G 43 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8397 (mmtm) REVERT: G 73 ASP cc_start: 0.8210 (t0) cc_final: 0.7857 (t0) REVERT: G 197 TYR cc_start: 0.6348 (m-80) cc_final: 0.6006 (m-80) REVERT: H 24 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7480 (mtp85) REVERT: H 104 ARG cc_start: 0.8719 (ptm-80) cc_final: 0.8083 (ptt90) REVERT: I 73 ASP cc_start: 0.8274 (t0) cc_final: 0.7778 (t0) REVERT: I 146 LYS cc_start: 0.8083 (tttp) cc_final: 0.7737 (tttp) REVERT: I 147 ASP cc_start: 0.8535 (m-30) cc_final: 0.8304 (m-30) REVERT: I 197 TYR cc_start: 0.6938 (m-80) cc_final: 0.6563 (m-80) REVERT: I 211 ASP cc_start: 0.6897 (m-30) cc_final: 0.6475 (t0) REVERT: K 73 ASP cc_start: 0.8176 (t0) cc_final: 0.7870 (t0) REVERT: K 99 MET cc_start: 0.9132 (mmt) cc_final: 0.8763 (mmt) REVERT: K 146 LYS cc_start: 0.7846 (tttp) cc_final: 0.7637 (tttp) REVERT: J 143 ARG cc_start: 0.8843 (tpt-90) cc_final: 0.8573 (tpt170) REVERT: L 106 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: L 108 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8462 (tptt) outliers start: 53 outliers final: 41 residues processed: 172 average time/residue: 0.3962 time to fit residues: 101.7866 Evaluate side-chains 172 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 184 HIS Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 31 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 216 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 27 optimal weight: 0.0980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN E 296 GLN K 158 ASN J 37 GLN L 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.049309 restraints weight = 62910.234| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.42 r_work: 0.2549 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22623 Z= 0.145 Angle : 0.586 22.371 30723 Z= 0.283 Chirality : 0.043 0.182 3537 Planarity : 0.004 0.050 3900 Dihedral : 7.098 58.331 3992 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.89 % Allowed : 12.46 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2760 helix: 2.22 (0.26), residues: 426 sheet: 0.81 (0.18), residues: 921 loop : -1.14 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J 149 HIS 0.004 0.001 HIS K 203 PHE 0.010 0.001 PHE K 68 TYR 0.012 0.001 TYR K 197 ARG 0.006 0.000 ARG I 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4456.96 seconds wall clock time: 88 minutes 2.83 seconds (5282.83 seconds total)