Starting phenix.real_space_refine on Sun Sep 13 09:57:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hjp_0235/09_2026/6hjp_0235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjp_0235/09_2026/6hjp_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/cci-nas-00/data/ceres_data/6hjp_0235/09_2026/6hjp_0235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2026/6hjp_0235.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2026/6hjp_0235.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2026/6hjp_0235.cif" model { file = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2026/6hjp_0235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2026/6hjp_0235.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 18 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: 18 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: 18 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.06, per 1000 atoms: 0.23 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: 2.33 Conformation dependent library (CDL) restraints added in 1.2 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: 0.93 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: 4.35 Time building geometry restraints manager: 2.97 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 - 15.99: 12083 15.99 - 31.98: 809 31.98 - 47.97: 176 47.97 - 63.96: 27 63.96 - 79.95: 18 Dihedral angle restraints: 13113 sinusoidal: 5103 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 13110 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: 0.05 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: 12.180 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.970 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 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 22701 Z= 0.523 Angle : 1.210 21.047 30927 Z= 0.703 Chirality : 0.088 0.840 3537 Planarity : 0.018 0.292 3900 Dihedral : 11.652 79.953 7905 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.89 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.001 ARG G 98 TYR 0.023 0.003 TYR B 141 PHE 0.017 0.003 PHE G 149 TRP 0.031 0.004 TRP E 153 HIS 0.009 0.002 HIS B 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00798 / 0.52 (22623) covalent geometry : angle 1.16975 / 0.70 (30723) SS BOND : bond 0.01537 / 1.03 ( 30) SS BOND : angle 2.09376 / 1.41 ( 60) hydrogen bonds : bond 0.17644 / 11.56 ( 792) hydrogen bonds : angle 7.25066 / 5.00 ( 2331) link_ALPHA1-3 : bond 0.03091 / 1.55 ( 3) link_ALPHA1-3 : angle 9.22831 / 5.25 ( 9) link_ALPHA1-6 : bond 0.00470 / 0.24 ( 3) link_ALPHA1-6 : angle 2.16631 / 1.40 ( 9) link_BETA1-4 : bond 0.00476 / 0.29 ( 24) link_BETA1-4 : angle 2.99672 / 2.01 ( 72) link_BETA1-6 : bond 0.00415 / 0.21 ( 3) link_BETA1-6 : angle 1.70213 / 0.80 ( 9) link_NAG-ASN : bond 0.00971 / 0.60 ( 15) link_NAG-ASN : angle 5.80914 / 4.04 ( 45) *********************** 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 to be fit. rotamer outliers: 57 poor density : 314 time to evaluate : 0.945 Fit side-chains 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: 0.8897 (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: 0.6150 (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: 0.7695 (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: 0.7334 (t0) REVERT: I 76 LYS cc_start: 0.9346 (mttt) cc_final: 0.9106 (mttm) REVERT: I 89 ASP cc_start: 0.9399 (p0) cc_final: 0.9076 (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: 0.6184 (t70) REVERT: I 212 LYS cc_start: 0.4815 (tppt) cc_final: 0.4614 (tptt) REVERT: I 215 GLU cc_start: 0.5643 (pt0) cc_final: 0.5417 (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: 0.1925 time to fit residues: 101.8960 Evaluate side-chains 173 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 184 HIS A 196 GLN A 250 ASN A 299 HIS A 323 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 114 GLN G 200 ASN H 6 GLN H 37 GLN H 156 GLN I 13 GLN I 114 GLN K 114 GLN J 6 GLN J 37 GLN J 167 GLN L 6 GLN L 37 GLN L 139 ASN L 156 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.047372 restraints weight = 63661.105| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.44 r_work: 0.2499 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22701 Z= 0.244 Angle : 0.779 14.783 30927 Z= 0.385 Chirality : 0.049 0.362 3537 Planarity : 0.005 0.062 3900 Dihedral : 6.412 55.165 3040 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.02 % Allowed : 9.47 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.15), residues: 2760 helix: 0.68 (0.25), residues: 423 sheet: -0.29 (0.17), residues: 906 loop : -2.06 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 87 TYR 0.018 0.002 TYR H 193 PHE 0.023 0.002 PHE I 68 TRP 0.018 0.002 TRP A 255 HIS 0.006 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (22623) covalent geometry : angle 0.75223 / 0.38 (30723) SS BOND : bond 0.00720 / 0.48 ( 30) SS BOND : angle 1.46969 / 0.99 ( 60) hydrogen bonds : bond 0.06595 / 4.36 ( 792) hydrogen bonds : angle 5.64232 / 3.90 ( 2331) link_ALPHA1-3 : bond 0.03040 / 1.51 ( 3) link_ALPHA1-3 : angle 4.08695 / 2.03 ( 9) link_ALPHA1-6 : bond 0.00442 / 0.22 ( 3) link_ALPHA1-6 : angle 1.45075 / 0.83 ( 9) link_BETA1-4 : bond 0.00864 / 0.61 ( 24) link_BETA1-4 : angle 2.61265 / 1.82 ( 72) link_BETA1-6 : bond 0.00823 / 0.41 ( 3) link_BETA1-6 : angle 1.49236 / 0.93 ( 9) link_NAG-ASN : bond 0.00353 / 0.21 ( 15) link_NAG-ASN : angle 3.51180 / 2.40 ( 45) *********************** 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 222 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 ARG cc_start: 0.8563 (ttm170) cc_final: 0.8256 (mtp180) REVERT: C 281 ARG cc_start: 0.8900 (mtp85) cc_final: 0.8695 (mtm-85) REVERT: E 230 MET cc_start: 0.9056 (mtp) cc_final: 0.8759 (mtp) REVERT: E 239 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8532 (mt0) REVERT: G 73 ASP cc_start: 0.8330 (t0) cc_final: 0.7848 (t0) REVERT: G 114 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8449 (tp-100) REVERT: G 197 TYR cc_start: 0.6981 (m-80) cc_final: 0.6261 (m-80) REVERT: G 202 ASN cc_start: 0.7722 (t0) cc_final: 0.7215 (p0) REVERT: G 213 ARG cc_start: 0.8022 (ttt180) cc_final: 0.7095 (tmt-80) REVERT: H 143 ARG cc_start: 0.8782 (tmt-80) cc_final: 0.8032 (tpt170) REVERT: H 166 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8892 (mp0) REVERT: I 1 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7952 (tm-30) REVERT: I 3 GLN cc_start: 0.8094 (pm20) cc_final: 0.7774 (pm20) REVERT: I 73 ASP cc_start: 0.8023 (t0) cc_final: 0.7288 (t0) REVERT: I 76 LYS cc_start: 0.9328 (mttt) cc_final: 0.9066 (mtpp) REVERT: I 87 ARG cc_start: 0.8640 (mtm-85) cc_final: 0.8389 (mtt-85) REVERT: I 89 ASP cc_start: 0.9399 (p0) cc_final: 0.9086 (p0) REVERT: I 146 LYS cc_start: 0.8190 (tttp) cc_final: 0.7807 (tttp) REVERT: I 147 ASP cc_start: 0.8367 (m-30) cc_final: 0.8070 (m-30) REVERT: I 211 ASP cc_start: 0.6569 (m-30) cc_final: 0.6130 (t0) REVERT: I 212 LYS cc_start: 0.5784 (tppt) cc_final: 0.5112 (mmmt) REVERT: I 215 GLU cc_start: 0.6219 (pt0) cc_final: 0.5458 (tp30) REVERT: K 73 ASP cc_start: 0.8433 (t0) cc_final: 0.7917 (t0) REVERT: K 89 ASP cc_start: 0.9348 (p0) cc_final: 0.9101 (p0) REVERT: K 99 MET cc_start: 0.9404 (mmt) cc_final: 0.9053 (mmt) REVERT: K 207 ASN cc_start: 0.8844 (m110) cc_final: 0.8624 (m-40) REVERT: J 108 LYS cc_start: 0.9097 (ttpt) cc_final: 0.8592 (tptt) REVERT: J 143 ARG cc_start: 0.8566 (tmt-80) cc_final: 0.8070 (tpt90) REVERT: J 191 LYS cc_start: 0.7355 (ttmp) cc_final: 0.6828 (tmtt) REVERT: L 24 ARG cc_start: 0.8420 (mtp-110) cc_final: 0.7776 (mtp-110) REVERT: L 70 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8434 (mm-30) REVERT: L 106 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: L 108 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8328 (tptt) REVERT: L 143 ARG cc_start: 0.8720 (tmt-80) cc_final: 0.8488 (tpt-90) outliers start: 48 outliers final: 25 residues processed: 209 average time/residue: 0.2027 time to fit residues: 61.5706 Evaluate side-chains 173 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 163 SER 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 103 GLU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain E residue 155 THR 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 98 LEU 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 48 ILE 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 30 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 177 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 228 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.0970 chunk 94 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 114 GLN J 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.076886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.049099 restraints weight = 63069.899| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.41 r_work: 0.2544 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22701 Z= 0.122 Angle : 0.655 17.490 30927 Z= 0.319 Chirality : 0.044 0.181 3537 Planarity : 0.004 0.057 3900 Dihedral : 5.625 45.549 3033 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.36 % Allowed : 9.43 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 2760 helix: 1.34 (0.25), residues: 423 sheet: -0.02 (0.17), residues: 930 loop : -1.71 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 211 TYR 0.011 0.001 TYR B 157 PHE 0.023 0.001 PHE H 140 TRP 0.012 0.001 TRP G 112 HIS 0.004 0.001 HIS L 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (22623) covalent geometry : angle 0.63794 / 0.32 (30723) SS BOND : bond 0.00457 / 0.31 ( 30) SS BOND : angle 0.92879 / 0.65 ( 60) hydrogen bonds : bond 0.05326 / 3.54 ( 792) hydrogen bonds : angle 5.12086 / 3.54 ( 2331) link_ALPHA1-3 : bond 0.02148 / 1.08 ( 3) link_ALPHA1-3 : angle 3.33100 / 1.83 ( 9) link_ALPHA1-6 : bond 0.00472 / 0.24 ( 3) link_ALPHA1-6 : angle 1.42236 / 0.84 ( 9) link_BETA1-4 : bond 0.00748 / 0.49 ( 24) link_BETA1-4 : angle 1.95632 / 1.32 ( 72) link_BETA1-6 : bond 0.00464 / 0.23 ( 3) link_BETA1-6 : angle 1.11135 / 0.69 ( 9) link_NAG-ASN : bond 0.00149 / 0.09 ( 15) link_NAG-ASN : angle 2.68149 / 1.83 ( 45) *********************** 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 214 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 158 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8559 (ttpp) REVERT: A 296 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8926 (tm130) REVERT: B 98 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9173 (tp) REVERT: C 211 ARG cc_start: 0.8525 (ttm170) cc_final: 0.8241 (mtp180) REVERT: D 127 ARG cc_start: 0.8656 (mpt-90) cc_final: 0.8041 (mtm110) REVERT: E 230 MET cc_start: 0.8995 (mtp) cc_final: 0.8778 (mtp) REVERT: G 73 ASP cc_start: 0.8303 (t0) cc_final: 0.7913 (t0) REVERT: G 202 ASN cc_start: 0.7684 (t0) cc_final: 0.6940 (p0) REVERT: H 4 MET cc_start: 0.8783 (mmm) cc_final: 0.8355 (mmm) REVERT: H 104 ARG cc_start: 0.8407 (ptm160) cc_final: 0.8184 (ptm160) REVERT: H 143 ARG cc_start: 0.8808 (tmt-80) cc_final: 0.8341 (tpt170) REVERT: H 166 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8864 (mp0) REVERT: I 73 ASP cc_start: 0.8017 (t0) cc_final: 0.7365 (t0) REVERT: I 76 LYS cc_start: 0.9301 (mttt) cc_final: 0.9066 (mtpp) REVERT: I 89 ASP cc_start: 0.9350 (p0) cc_final: 0.9023 (p0) REVERT: I 146 LYS cc_start: 0.8047 (tttp) cc_final: 0.7659 (tttp) REVERT: I 147 ASP cc_start: 0.8439 (m-30) cc_final: 0.8099 (m-30) REVERT: I 211 ASP cc_start: 0.6433 (m-30) cc_final: 0.6030 (t0) REVERT: I 212 LYS cc_start: 0.5815 (tppt) cc_final: 0.5119 (tptt) REVERT: I 215 GLU cc_start: 0.5911 (pt0) cc_final: 0.5272 (tp30) REVERT: K 73 ASP cc_start: 0.8296 (t0) cc_final: 0.7836 (t0) REVERT: K 89 ASP cc_start: 0.9320 (p0) cc_final: 0.9099 (p0) REVERT: K 99 MET cc_start: 0.9336 (mmt) cc_final: 0.9002 (mmt) REVERT: K 207 ASN cc_start: 0.8916 (m110) cc_final: 0.8662 (m-40) REVERT: J 108 LYS cc_start: 0.9143 (ttpt) cc_final: 0.8629 (tptt) REVERT: J 143 ARG cc_start: 0.8581 (tmt-80) cc_final: 0.8034 (tpt90) REVERT: J 191 LYS cc_start: 0.7420 (ttmp) cc_final: 0.7122 (tptt) REVERT: L 24 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.7789 (mtm110) REVERT: L 70 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8479 (mm-30) REVERT: L 106 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: L 108 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8285 (tptt) REVERT: L 143 ARG cc_start: 0.8666 (tmt-80) cc_final: 0.8119 (tpt170) outliers start: 56 outliers final: 27 residues processed: 204 average time/residue: 0.1931 time to fit residues: 57.5552 Evaluate side-chains 170 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 LYS Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 296 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 177 LEU Chi-restraints excluded: chain D residue 2 LEU 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 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 141 LEU Chi-restraints excluded: chain G residue 198 ILE Chi-restraints excluded: chain G residue 214 VAL 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 L residue 70 GLU 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 14 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 216 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 ASN C 231 ASN C 296 GLN E 150 ASN E 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.074908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.046960 restraints weight = 63529.794| |-----------------------------------------------------------------------------| r_work (start): 0.2635 rms_B_bonded: 3.42 r_work: 0.2486 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22701 Z= 0.224 Angle : 0.685 20.432 30927 Z= 0.336 Chirality : 0.045 0.182 3537 Planarity : 0.004 0.053 3900 Dihedral : 5.486 45.892 3028 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.33 % Favored : 94.64 % Rotamer: Outliers : 2.78 % Allowed : 10.14 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.16), residues: 2760 helix: 1.52 (0.25), residues: 423 sheet: 0.10 (0.17), residues: 945 loop : -1.53 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 98 TYR 0.015 0.002 TYR C 102 PHE 0.022 0.002 PHE I 68 TRP 0.024 0.001 TRP J 149 HIS 0.006 0.002 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (22623) covalent geometry : angle 0.66744 / 0.33 (30723) SS BOND : bond 0.00583 / 0.38 ( 30) SS BOND : angle 1.15019 / 0.77 ( 60) hydrogen bonds : bond 0.05723 / 3.80 ( 792) hydrogen bonds : angle 5.04217 / 3.48 ( 2331) link_ALPHA1-3 : bond 0.01712 / 0.86 ( 3) link_ALPHA1-3 : angle 3.07133 / 1.79 ( 9) link_ALPHA1-6 : bond 0.00548 / 0.28 ( 3) link_ALPHA1-6 : angle 1.55456 / 0.89 ( 9) link_BETA1-4 : bond 0.00665 / 0.42 ( 24) link_BETA1-4 : angle 1.94567 / 1.33 ( 72) link_BETA1-6 : bond 0.00547 / 0.27 ( 3) link_BETA1-6 : angle 1.07236 / 0.64 ( 9) link_NAG-ASN : bond 0.00321 / 0.19 ( 15) link_NAG-ASN : angle 2.84381 / 1.93 ( 45) *********************** 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 205 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8778 (OUTLIER) cc_final: 0.7840 (p90) REVERT: B 98 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9169 (tp) REVERT: C 49 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9062 (mm) REVERT: C 184 HIS cc_start: 0.8652 (OUTLIER) cc_final: 0.7661 (p90) REVERT: C 211 ARG cc_start: 0.8604 (ttm170) cc_final: 0.8328 (mtp180) REVERT: E 49 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8959 (mm) REVERT: G 43 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8170 (mmtm) REVERT: G 73 ASP cc_start: 0.8174 (t0) cc_final: 0.7821 (t0) REVERT: G 202 ASN cc_start: 0.7586 (t0) cc_final: 0.6863 (p0) REVERT: G 213 ARG cc_start: 0.7975 (ttt180) cc_final: 0.7330 (tmt-80) REVERT: H 4 MET cc_start: 0.8908 (mmm) cc_final: 0.8320 (mmm) REVERT: H 24 ARG cc_start: 0.8364 (mtp85) cc_final: 0.7780 (mtp-110) REVERT: I 1 GLU cc_start: 0.8844 (tp30) cc_final: 0.8403 (tm-30) REVERT: I 73 ASP cc_start: 0.8119 (t0) cc_final: 0.7463 (t0) REVERT: I 76 LYS cc_start: 0.9329 (mttt) cc_final: 0.9104 (mtpp) REVERT: I 146 LYS cc_start: 0.7998 (tttp) cc_final: 0.7609 (tttp) REVERT: I 211 ASP cc_start: 0.6551 (m-30) cc_final: 0.6134 (t0) REVERT: I 212 LYS cc_start: 0.5912 (tppt) cc_final: 0.5175 (mmmt) REVERT: I 215 GLU cc_start: 0.5777 (pt0) cc_final: 0.5104 (tp30) REVERT: K 73 ASP cc_start: 0.8306 (t0) cc_final: 0.7914 (t0) REVERT: K 99 MET cc_start: 0.9358 (mmt) cc_final: 0.8941 (mmt) REVERT: K 207 ASN cc_start: 0.8844 (m110) cc_final: 0.8588 (m-40) REVERT: J 108 LYS cc_start: 0.9077 (ttpt) cc_final: 0.8582 (tptt) REVERT: J 211 ASN cc_start: 0.6618 (m110) cc_final: 0.6328 (m110) REVERT: L 106 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: L 108 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8295 (tptt) outliers start: 66 outliers final: 35 residues processed: 195 average time/residue: 0.1876 time to fit residues: 53.7252 Evaluate side-chains 170 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 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 B residue 173 ILE 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 D residue 2 LEU 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 155 THR 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 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 197 TYR 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 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 L residue 106 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 130 optimal weight: 0.1980 chunk 233 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS C 32 HIS C 283 GLN C 296 GLN I 158 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.047273 restraints weight = 63250.384| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.41 r_work: 0.2492 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22701 Z= 0.184 Angle : 0.657 22.543 30927 Z= 0.319 Chirality : 0.044 0.176 3537 Planarity : 0.004 0.051 3900 Dihedral : 5.218 41.908 3026 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.69 % Allowed : 10.86 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 2760 helix: 1.75 (0.25), residues: 423 sheet: 0.22 (0.17), residues: 951 loop : -1.40 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 143 TYR 0.012 0.001 TYR K 197 PHE 0.018 0.002 PHE H 140 TRP 0.016 0.001 TRP J 149 HIS 0.005 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (22623) covalent geometry : angle 0.63887 / 0.31 (30723) SS BOND : bond 0.00510 / 0.34 ( 30) SS BOND : angle 1.62283 / 1.06 ( 60) hydrogen bonds : bond 0.05381 / 3.57 ( 792) hydrogen bonds : angle 4.85867 / 3.35 ( 2331) link_ALPHA1-3 : bond 0.01248 / 0.63 ( 3) link_ALPHA1-3 : angle 2.53439 / 1.52 ( 9) link_ALPHA1-6 : bond 0.00454 / 0.23 ( 3) link_ALPHA1-6 : angle 1.62005 / 0.92 ( 9) link_BETA1-4 : bond 0.00661 / 0.42 ( 24) link_BETA1-4 : angle 1.86680 / 1.27 ( 72) link_BETA1-6 : bond 0.00514 / 0.26 ( 3) link_BETA1-6 : angle 1.03133 / 0.63 ( 9) link_NAG-ASN : bond 0.00219 / 0.13 ( 15) link_NAG-ASN : angle 2.62456 / 1.78 ( 45) *********************** 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 202 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 138 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.7811 (p90) REVERT: A 192 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8809 (tm-30) REVERT: C 184 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.7665 (p90) REVERT: C 211 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8388 (mtp180) REVERT: E 242 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8919 (t) REVERT: G 43 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8271 (mmtm) REVERT: G 73 ASP cc_start: 0.8130 (t0) cc_final: 0.7721 (t0) REVERT: G 202 ASN cc_start: 0.7544 (t0) cc_final: 0.6768 (p0) REVERT: G 213 ARG cc_start: 0.8004 (ttt180) cc_final: 0.7365 (tmt-80) REVERT: H 4 MET cc_start: 0.8859 (mmm) cc_final: 0.8321 (mmm) REVERT: H 24 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7183 (mtp85) REVERT: I 73 ASP cc_start: 0.8127 (t0) cc_final: 0.7467 (t0) REVERT: I 76 LYS cc_start: 0.9328 (mttt) cc_final: 0.9115 (mtpp) REVERT: I 146 LYS cc_start: 0.7977 (tttp) cc_final: 0.7610 (tttp) REVERT: I 197 TYR cc_start: 0.7371 (m-80) cc_final: 0.7106 (m-80) REVERT: I 211 ASP cc_start: 0.6578 (m-30) cc_final: 0.6144 (t0) REVERT: I 212 LYS cc_start: 0.6008 (tppt) cc_final: 0.5168 (mmmt) REVERT: I 215 GLU cc_start: 0.5654 (pt0) cc_final: 0.5033 (tp30) REVERT: K 73 ASP cc_start: 0.8209 (t0) cc_final: 0.7789 (t0) REVERT: K 99 MET cc_start: 0.9344 (mmt) cc_final: 0.8957 (mmt) REVERT: K 207 ASN cc_start: 0.8845 (m110) cc_final: 0.8483 (p0) REVERT: J 108 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8589 (tptt) REVERT: J 211 ASN cc_start: 0.6417 (m110) cc_final: 0.6126 (m110) REVERT: L 24 ARG cc_start: 0.8425 (mtp-110) cc_final: 0.8216 (mtp-110) REVERT: L 106 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: L 108 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8305 (tptt) outliers start: 64 outliers final: 39 residues processed: 190 average time/residue: 0.1778 time to fit residues: 50.4228 Evaluate side-chains 176 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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 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 B residue 173 ILE 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 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 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 148 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 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 Chi-restraints excluded: chain L residue 190 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 1 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 233 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 ASN A 183 HIS B 128 ASN C 150 ASN C 183 HIS C 283 GLN C 296 GLN D 128 ASN E 231 ASN E 296 GLN L 159 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.046243 restraints weight = 63448.473| |-----------------------------------------------------------------------------| r_work (start): 0.2611 rms_B_bonded: 3.42 r_work: 0.2460 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22701 Z= 0.244 Angle : 0.686 24.220 30927 Z= 0.336 Chirality : 0.045 0.185 3537 Planarity : 0.004 0.050 3900 Dihedral : 5.374 47.796 3026 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.11 % Allowed : 10.73 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.16), residues: 2760 helix: 1.71 (0.25), residues: 423 sheet: 0.30 (0.17), residues: 942 loop : -1.37 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 98 TYR 0.014 0.002 TYR A 102 PHE 0.022 0.002 PHE C 115 TRP 0.038 0.001 TRP J 149 HIS 0.007 0.002 HIS C 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.24 (22623) covalent geometry : angle 0.66927 / 0.33 (30723) SS BOND : bond 0.00607 / 0.40 ( 30) SS BOND : angle 1.55293 / 0.99 ( 60) hydrogen bonds : bond 0.05761 / 3.82 ( 792) hydrogen bonds : angle 4.90219 / 3.39 ( 2331) link_ALPHA1-3 : bond 0.00952 / 0.48 ( 3) link_ALPHA1-3 : angle 1.88556 / 1.16 ( 9) link_ALPHA1-6 : bond 0.00519 / 0.26 ( 3) link_ALPHA1-6 : angle 1.70748 / 0.95 ( 9) link_BETA1-4 : bond 0.00634 / 0.40 ( 24) link_BETA1-4 : angle 1.89798 / 1.30 ( 72) link_BETA1-6 : bond 0.00516 / 0.26 ( 3) link_BETA1-6 : angle 1.04549 / 0.63 ( 9) link_NAG-ASN : bond 0.00366 / 0.22 ( 15) link_NAG-ASN : angle 2.73915 / 1.85 ( 45) *********************** 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 211 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 137 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.9013 (OUTLIER) cc_final: 0.7817 (p90) REVERT: A 192 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8854 (tm-30) REVERT: C 184 HIS cc_start: 0.8845 (OUTLIER) cc_final: 0.7654 (p90) REVERT: C 211 ARG cc_start: 0.8656 (ttm170) cc_final: 0.8405 (mtp180) REVERT: E 242 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8864 (t) REVERT: G 43 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8365 (mmtm) REVERT: G 73 ASP cc_start: 0.8107 (t0) cc_final: 0.7660 (t0) REVERT: H 4 MET cc_start: 0.8962 (mmm) cc_final: 0.8333 (mmm) REVERT: H 24 ARG cc_start: 0.8347 (mtp85) cc_final: 0.7742 (mtp-110) REVERT: H 79 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: I 73 ASP cc_start: 0.8076 (t0) cc_final: 0.7407 (t0) REVERT: I 76 LYS cc_start: 0.9352 (mttt) cc_final: 0.9128 (mtpp) REVERT: I 80 TYR cc_start: 0.9193 (m-80) cc_final: 0.8990 (m-80) REVERT: I 146 LYS cc_start: 0.7990 (tttp) cc_final: 0.7721 (tttp) REVERT: I 197 TYR cc_start: 0.7310 (m-80) cc_final: 0.7039 (m-80) REVERT: I 211 ASP cc_start: 0.6805 (m-30) cc_final: 0.6456 (t0) REVERT: I 215 GLU cc_start: 0.5660 (pt0) cc_final: 0.5098 (tp30) REVERT: K 73 ASP cc_start: 0.8147 (t0) cc_final: 0.7671 (t0) REVERT: K 99 MET cc_start: 0.9358 (mmt) cc_final: 0.8950 (mmt) REVERT: K 126 LYS cc_start: 0.8321 (tptp) cc_final: 0.7841 (tmtt) REVERT: K 207 ASN cc_start: 0.8879 (m110) cc_final: 0.8559 (p0) REVERT: J 211 ASN cc_start: 0.6335 (m110) cc_final: 0.6084 (m110) REVERT: L 24 ARG cc_start: 0.8442 (mtp-110) cc_final: 0.8176 (mtp-110) REVERT: L 106 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: L 108 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8313 (tptt) outliers start: 74 outliers final: 49 residues processed: 199 average time/residue: 0.1952 time to fit residues: 57.0610 Evaluate side-chains 184 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 130 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 163 SER Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 5 ASP 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 C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU 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 103 GLU Chi-restraints excluded: chain F residue 163 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 103 MET Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 197 TYR 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 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 106 GLU Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 190 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 108 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 111 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 272 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 166 optimal weight: 0.5980 chunk 265 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 296 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN J 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.076210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.048411 restraints weight = 62927.022| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.40 r_work: 0.2526 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22701 Z= 0.114 Angle : 0.614 23.879 30927 Z= 0.294 Chirality : 0.043 0.210 3537 Planarity : 0.004 0.050 3900 Dihedral : 4.903 42.619 3026 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.23 % Allowed : 11.70 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2760 helix: 2.10 (0.26), residues: 423 sheet: 0.46 (0.17), residues: 942 loop : -1.25 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 100 TYR 0.011 0.001 TYR B 157 PHE 0.013 0.001 PHE H 140 TRP 0.022 0.001 TRP J 149 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (22623) covalent geometry : angle 0.59928 / 0.29 (30723) SS BOND : bond 0.00369 / 0.25 ( 30) SS BOND : angle 1.30160 / 0.83 ( 60) hydrogen bonds : bond 0.04836 / 3.22 ( 792) hydrogen bonds : angle 4.60997 / 3.17 ( 2331) link_ALPHA1-3 : bond 0.00919 / 0.46 ( 3) link_ALPHA1-3 : angle 1.42487 / 0.88 ( 9) link_ALPHA1-6 : bond 0.00375 / 0.19 ( 3) link_ALPHA1-6 : angle 1.55098 / 0.90 ( 9) link_BETA1-4 : bond 0.00660 / 0.43 ( 24) link_BETA1-4 : angle 1.81657 / 1.25 ( 72) link_BETA1-6 : bond 0.00512 / 0.26 ( 3) link_BETA1-6 : angle 1.04920 / 0.64 ( 9) link_NAG-ASN : bond 0.00134 / 0.08 ( 15) link_NAG-ASN : angle 2.22940 / 1.52 ( 45) *********************** 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 190 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.7705 (p90) REVERT: A 192 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8817 (tm-30) REVERT: C 184 HIS cc_start: 0.8596 (OUTLIER) cc_final: 0.7537 (p90) REVERT: C 211 ARG cc_start: 0.8596 (ttm170) cc_final: 0.8374 (mtp180) REVERT: G 43 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8239 (mmtm) REVERT: G 73 ASP cc_start: 0.8092 (t0) cc_final: 0.7614 (t0) REVERT: H 4 MET cc_start: 0.8839 (mmm) cc_final: 0.8579 (mmm) REVERT: H 24 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7145 (mtp85) REVERT: I 73 ASP cc_start: 0.8021 (t0) cc_final: 0.7363 (t0) REVERT: I 76 LYS cc_start: 0.9353 (mttt) cc_final: 0.9137 (mtpp) REVERT: I 197 TYR cc_start: 0.7225 (m-80) cc_final: 0.6953 (m-80) REVERT: I 211 ASP cc_start: 0.6694 (m-30) cc_final: 0.6328 (t0) REVERT: I 215 GLU cc_start: 0.5670 (pt0) cc_final: 0.5080 (tp30) REVERT: K 73 ASP cc_start: 0.8167 (t0) cc_final: 0.7683 (t0) REVERT: K 99 MET cc_start: 0.9320 (mmt) cc_final: 0.8951 (mmt) REVERT: K 126 LYS cc_start: 0.8388 (tptp) cc_final: 0.8047 (tptp) REVERT: K 207 ASN cc_start: 0.8850 (m110) cc_final: 0.8597 (m-40) REVERT: J 143 ARG cc_start: 0.8636 (tmt-80) cc_final: 0.8331 (tpt170) REVERT: J 211 ASN cc_start: 0.6312 (m110) cc_final: 0.6041 (m110) REVERT: L 24 ARG cc_start: 0.8360 (mtp-110) cc_final: 0.8137 (mtp-110) REVERT: L 108 LYS cc_start: 0.8973 (ttpt) cc_final: 0.8321 (tptt) REVERT: L 109 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7461 (ptm-80) outliers start: 53 outliers final: 35 residues processed: 181 average time/residue: 0.1938 time to fit residues: 51.5200 Evaluate side-chains 166 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 128 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 B residue 166 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 184 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 2 LEU 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 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 4 LEU Chi-restraints excluded: chain G residue 79 LEU 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 151 VAL Chi-restraints excluded: chain H residue 190 HIS 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 37 GLN Chi-restraints excluded: chain L residue 109 ARG 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 74 optimal weight: 1.9990 chunk 148 optimal weight: 0.2980 chunk 201 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 259 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 166 optimal weight: 0.0060 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN C 296 GLN E 296 GLN F 128 ASN H 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 = 0.3337 r_free = 0.3337 target = 0.076297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.048449 restraints weight = 62952.176| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.41 r_work: 0.2528 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22701 Z= 0.119 Angle : 0.600 23.530 30927 Z= 0.288 Chirality : 0.042 0.192 3537 Planarity : 0.004 0.052 3900 Dihedral : 4.766 42.628 3026 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.27 % Allowed : 11.91 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2760 helix: 2.19 (0.26), residues: 423 sheet: 0.55 (0.17), residues: 942 loop : -1.18 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 100 TYR 0.012 0.001 TYR K 197 PHE 0.012 0.001 PHE H 140 TRP 0.020 0.001 TRP J 149 HIS 0.004 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (22623) covalent geometry : angle 0.58627 / 0.28 (30723) SS BOND : bond 0.00388 / 0.26 ( 30) SS BOND : angle 1.20911 / 0.79 ( 60) hydrogen bonds : bond 0.04755 / 3.17 ( 792) hydrogen bonds : angle 4.50977 / 3.11 ( 2331) link_ALPHA1-3 : bond 0.00887 / 0.44 ( 3) link_ALPHA1-3 : angle 1.33107 / 0.81 ( 9) link_ALPHA1-6 : bond 0.00420 / 0.21 ( 3) link_ALPHA1-6 : angle 1.48525 / 0.88 ( 9) link_BETA1-4 : bond 0.00635 / 0.41 ( 24) link_BETA1-4 : angle 1.80438 / 1.24 ( 72) link_BETA1-6 : bond 0.00501 / 0.25 ( 3) link_BETA1-6 : angle 1.05446 / 0.65 ( 9) link_NAG-ASN : bond 0.00122 / 0.07 ( 15) link_NAG-ASN : angle 2.18272 / 1.49 ( 45) *********************** 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 188 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 134 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8764 (OUTLIER) cc_final: 0.7786 (p90) REVERT: A 192 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8786 (tm-30) REVERT: C 184 HIS cc_start: 0.8582 (OUTLIER) cc_final: 0.7618 (p90) REVERT: C 211 ARG cc_start: 0.8596 (ttm170) cc_final: 0.8395 (mtp180) REVERT: G 43 LYS cc_start: 0.8673 (mmtp) cc_final: 0.8325 (mmtm) REVERT: G 73 ASP cc_start: 0.8131 (t0) cc_final: 0.7688 (t0) REVERT: H 4 MET cc_start: 0.8870 (mmm) cc_final: 0.8346 (mmm) REVERT: H 24 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7130 (mtp85) REVERT: I 73 ASP cc_start: 0.8112 (t0) cc_final: 0.7461 (t0) REVERT: I 76 LYS cc_start: 0.9360 (mttt) cc_final: 0.9157 (mtpp) REVERT: I 197 TYR cc_start: 0.7248 (m-80) cc_final: 0.7008 (m-80) REVERT: I 211 ASP cc_start: 0.6681 (m-30) cc_final: 0.6325 (t0) REVERT: I 215 GLU cc_start: 0.5701 (pt0) cc_final: 0.5085 (tp30) REVERT: K 73 ASP cc_start: 0.8169 (t0) cc_final: 0.7735 (t0) REVERT: K 99 MET cc_start: 0.9317 (mmt) cc_final: 0.8913 (mmt) REVERT: K 207 ASN cc_start: 0.8828 (m110) cc_final: 0.8563 (m-40) REVERT: J 143 ARG cc_start: 0.8646 (tmt-80) cc_final: 0.8331 (tpt170) REVERT: L 24 ARG cc_start: 0.8378 (mtp-110) cc_final: 0.8146 (mtp-110) REVERT: L 108 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8434 (tptt) outliers start: 54 outliers final: 38 residues processed: 180 average time/residue: 0.1921 time to fit residues: 51.2676 Evaluate side-chains 165 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE 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 98 LEU Chi-restraints excluded: chain D residue 163 SER 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 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 4 LEU Chi-restraints excluded: chain G residue 79 LEU 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 151 VAL Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain H residue 190 HIS 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 187 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 184 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 237 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN C 296 GLN E 183 HIS H 37 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 ASN J 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.073765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.045884 restraints weight = 63345.123| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 3.39 r_work: 0.2454 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 22701 Z= 0.291 Angle : 0.712 24.850 30927 Z= 0.350 Chirality : 0.046 0.208 3537 Planarity : 0.004 0.051 3900 Dihedral : 5.323 51.006 3026 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.44 % Allowed : 11.83 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2760 helix: 1.77 (0.26), residues: 426 sheet: 0.51 (0.17), residues: 921 loop : -1.32 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 101 TYR 0.015 0.002 TYR K 197 PHE 0.027 0.002 PHE K 68 TRP 0.018 0.001 TRP J 149 HIS 0.006 0.002 HIS C 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.29 (22623) covalent geometry : angle 0.69583 / 0.35 (30723) SS BOND : bond 0.00658 / 0.43 ( 30) SS BOND : angle 1.66214 / 1.08 ( 60) hydrogen bonds : bond 0.05933 / 3.94 ( 792) hydrogen bonds : angle 4.81361 / 3.33 ( 2331) link_ALPHA1-3 : bond 0.00766 / 0.39 ( 3) link_ALPHA1-3 : angle 1.42352 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00475 / 0.24 ( 3) link_ALPHA1-6 : angle 1.58500 / 0.89 ( 9) link_BETA1-4 : bond 0.00590 / 0.38 ( 24) link_BETA1-4 : angle 1.89741 / 1.30 ( 72) link_BETA1-6 : bond 0.00510 / 0.26 ( 3) link_BETA1-6 : angle 1.00789 / 0.60 ( 9) link_NAG-ASN : bond 0.00469 / 0.27 ( 15) link_NAG-ASN : angle 2.70219 / 1.83 ( 45) *********************** 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 to be fit. rotamer outliers: 58 poor density : 127 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.9064 (OUTLIER) cc_final: 0.7860 (p90) REVERT: A 192 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8881 (tm-30) REVERT: B 59 MET cc_start: 0.8711 (mmm) cc_final: 0.8403 (mmt) REVERT: C 184 HIS cc_start: 0.8897 (OUTLIER) cc_final: 0.7825 (p90) REVERT: C 211 ARG cc_start: 0.8681 (ttm170) cc_final: 0.8444 (mtp180) REVERT: D 59 MET cc_start: 0.8582 (mmm) cc_final: 0.7957 (mmm) REVERT: G 43 LYS cc_start: 0.8799 (mmtp) cc_final: 0.8479 (mmtm) REVERT: G 73 ASP cc_start: 0.8205 (t0) cc_final: 0.7751 (t0) REVERT: H 4 MET cc_start: 0.9021 (mmm) cc_final: 0.8236 (mmm) REVERT: H 24 ARG cc_start: 0.8355 (mtp85) cc_final: 0.7946 (mtp-110) REVERT: I 43 LYS cc_start: 0.8865 (mmtp) cc_final: 0.8460 (mmtm) REVERT: I 73 ASP cc_start: 0.8100 (t0) cc_final: 0.7430 (t0) REVERT: I 76 LYS cc_start: 0.9368 (mttt) cc_final: 0.9165 (mtpp) REVERT: I 146 LYS cc_start: 0.7975 (tttp) cc_final: 0.7665 (tttp) REVERT: I 197 TYR cc_start: 0.7287 (m-80) cc_final: 0.7000 (m-80) REVERT: K 73 ASP cc_start: 0.8202 (t0) cc_final: 0.7800 (t0) REVERT: K 99 MET cc_start: 0.9350 (mmt) cc_final: 0.8925 (mmt) REVERT: K 207 ASN cc_start: 0.8862 (m110) cc_final: 0.8574 (p0) REVERT: L 24 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.8233 (mtp-110) REVERT: L 108 LYS cc_start: 0.9091 (ttpt) cc_final: 0.8510 (tptt) outliers start: 58 outliers final: 38 residues processed: 178 average time/residue: 0.1846 time to fit residues: 49.2299 Evaluate side-chains 163 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 166 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 C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU 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 109 LEU Chi-restraints excluded: chain E residue 155 THR 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 G residue 4 LEU 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 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 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 187 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 105 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 189 optimal weight: 10.0000 chunk 204 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN C 296 GLN E 296 GLN H 37 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 158 ASN J 37 GLN L 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.048035 restraints weight = 62863.910| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.39 r_work: 0.2515 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22701 Z= 0.116 Angle : 0.621 24.581 30927 Z= 0.298 Chirality : 0.043 0.198 3537 Planarity : 0.004 0.049 3900 Dihedral : 4.932 45.585 3026 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.89 % Allowed : 12.33 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.16), residues: 2760 helix: 2.03 (0.26), residues: 426 sheet: 0.62 (0.17), residues: 936 loop : -1.20 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 101 TYR 0.013 0.001 TYR H 36 PHE 0.013 0.001 PHE H 140 TRP 0.019 0.001 TRP J 149 HIS 0.004 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (22623) covalent geometry : angle 0.60684 / 0.29 (30723) SS BOND : bond 0.00390 / 0.26 ( 30) SS BOND : angle 1.42895 / 0.91 ( 60) hydrogen bonds : bond 0.04949 / 3.30 ( 792) hydrogen bonds : angle 4.55447 / 3.14 ( 2331) link_ALPHA1-3 : bond 0.00897 / 0.45 ( 3) link_ALPHA1-3 : angle 1.27624 / 0.78 ( 9) link_ALPHA1-6 : bond 0.00466 / 0.24 ( 3) link_ALPHA1-6 : angle 1.53853 / 0.90 ( 9) link_BETA1-4 : bond 0.00642 / 0.42 ( 24) link_BETA1-4 : angle 1.78429 / 1.22 ( 72) link_BETA1-6 : bond 0.00491 / 0.25 ( 3) link_BETA1-6 : angle 1.02857 / 0.64 ( 9) link_NAG-ASN : bond 0.00140 / 0.08 ( 15) link_NAG-ASN : angle 2.18047 / 1.48 ( 45) ********************** 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 176 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.782 Fit side-chains REVERT: A 184 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.7718 (p90) REVERT: A 192 GLN cc_start: 0.9100 (tm-30) cc_final: 0.8840 (tm-30) REVERT: C 184 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.7589 (p90) REVERT: C 211 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8354 (mtp180) REVERT: D 59 MET cc_start: 0.8464 (mmm) cc_final: 0.8185 (mmm) REVERT: G 43 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8443 (mmtp) REVERT: G 73 ASP cc_start: 0.8172 (t0) cc_final: 0.7727 (t0) REVERT: H 4 MET cc_start: 0.8868 (mmm) cc_final: 0.8549 (mmm) REVERT: H 24 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7144 (mtp85) REVERT: I 73 ASP cc_start: 0.8085 (t0) cc_final: 0.7407 (t0) REVERT: I 76 LYS cc_start: 0.9351 (mttt) cc_final: 0.9146 (mtpp) REVERT: I 146 LYS cc_start: 0.7900 (tttp) cc_final: 0.7599 (tttp) REVERT: I 197 TYR cc_start: 0.7213 (m-80) cc_final: 0.6968 (m-80) REVERT: I 211 ASP cc_start: 0.6824 (m-30) cc_final: 0.6426 (t0) REVERT: K 6 GLU cc_start: 0.7941 (pm20) cc_final: 0.7380 (pm20) REVERT: K 73 ASP cc_start: 0.8124 (t0) cc_final: 0.7626 (t0) REVERT: K 99 MET cc_start: 0.9324 (mmt) cc_final: 0.8932 (mmt) REVERT: K 126 LYS cc_start: 0.8122 (tptp) cc_final: 0.7854 (tptp) REVERT: K 207 ASN cc_start: 0.8830 (m110) cc_final: 0.8587 (m-40) REVERT: J 143 ARG cc_start: 0.8614 (tmt-80) cc_final: 0.8139 (tpt170) REVERT: L 24 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8167 (mtp-110) REVERT: L 108 LYS cc_start: 0.9046 (ttpt) cc_final: 0.8431 (tptt) outliers start: 45 outliers final: 34 residues processed: 169 average time/residue: 0.1837 time to fit residues: 46.3681 Evaluate side-chains 163 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 169 THR Chi-restraints excluded: chain A residue 184 HIS 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 166 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 C residue 184 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain D residue 2 LEU 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 155 THR 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 98 LEU Chi-restraints excluded: chain G residue 4 LEU 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 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 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 187 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 190 optimal weight: 0.0040 chunk 150 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 chunk 58 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 14 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 GLN C 296 GLN E 296 GLN H 37 GLN H 156 GLN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.076548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.048784 restraints weight = 62747.858| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 3.39 r_work: 0.2536 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22701 Z= 0.115 Angle : 0.598 23.534 30927 Z= 0.287 Chirality : 0.042 0.185 3537 Planarity : 0.004 0.054 3900 Dihedral : 4.666 43.290 3026 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.94 % Allowed : 12.25 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.16), residues: 2760 helix: 2.23 (0.26), residues: 426 sheet: 0.73 (0.18), residues: 930 loop : -1.14 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 143 TYR 0.020 0.001 TYR I 179 PHE 0.013 0.001 PHE K 68 TRP 0.017 0.001 TRP J 149 HIS 0.004 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (22623) covalent geometry : angle 0.58430 / 0.28 (30723) SS BOND : bond 0.00351 / 0.23 ( 30) SS BOND : angle 1.27950 / 0.82 ( 60) hydrogen bonds : bond 0.04611 / 3.07 ( 792) hydrogen bonds : angle 4.39268 / 3.02 ( 2331) link_ALPHA1-3 : bond 0.00906 / 0.45 ( 3) link_ALPHA1-3 : angle 1.26962 / 0.75 ( 9) link_ALPHA1-6 : bond 0.00459 / 0.23 ( 3) link_ALPHA1-6 : angle 1.42127 / 0.86 ( 9) link_BETA1-4 : bond 0.00621 / 0.40 ( 24) link_BETA1-4 : angle 1.77821 / 1.22 ( 72) link_BETA1-6 : bond 0.00501 / 0.25 ( 3) link_BETA1-6 : angle 1.06755 / 0.67 ( 9) link_NAG-ASN : bond 0.00108 / 0.07 ( 15) link_NAG-ASN : angle 2.03305 / 1.38 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5258.50 seconds wall clock time: 91 minutes 31.70 seconds (5491.70 seconds total)