Starting phenix.real_space_refine on Fri Sep 19 02:59:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hjp_0235/09_2025/6hjp_0235.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hjp_0235/09_2025/6hjp_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 { model { file = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2025/6hjp_0235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2025/6hjp_0235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2025/6hjp_0235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hjp_0235/09_2025/6hjp_0235.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.41, per 1000 atoms: 0.20 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: 1.85 Conformation dependent library (CDL) restraints added in 803.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.87 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: 4.10 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4368 1.32 - 1.45: 5889 1.45 - 1.57: 12246 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22623 Sorted by residual: bond pdb=" N GLU B 139 " pdb=" CA GLU B 139 " ideal model delta sigma weight residual 1.459 1.396 0.063 9.10e-03 1.21e+04 4.76e+01 bond pdb=" N GLU F 139 " pdb=" CA GLU F 139 " ideal model delta sigma weight residual 1.459 1.397 0.063 9.10e-03 1.21e+04 4.75e+01 bond pdb=" N GLU D 139 " pdb=" CA GLU D 139 " ideal model delta sigma weight residual 1.459 1.397 0.062 9.10e-03 1.21e+04 4.65e+01 bond pdb=" N HIS D 142 " pdb=" CA HIS D 142 " ideal model delta sigma weight residual 1.456 1.415 0.042 1.14e-02 7.69e+03 1.33e+01 bond pdb=" N HIS F 142 " pdb=" CA HIS F 142 " ideal model delta sigma weight residual 1.456 1.415 0.042 1.14e-02 7.69e+03 1.33e+01 ... (remaining 22618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 28288 2.03 - 4.05: 2168 4.05 - 6.08: 210 6.08 - 8.10: 48 8.10 - 10.13: 9 Bond angle restraints: 30723 Sorted by residual: angle pdb=" CA PHE F 140 " pdb=" CB PHE F 140 " pdb=" CG PHE F 140 " ideal model delta sigma weight residual 113.80 107.03 6.77 1.00e+00 1.00e+00 4.58e+01 angle pdb=" CA PHE D 140 " pdb=" CB PHE D 140 " pdb=" CG PHE D 140 " ideal model delta sigma weight residual 113.80 107.07 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" CA PHE B 140 " pdb=" CB PHE B 140 " pdb=" CG PHE B 140 " ideal model delta sigma weight residual 113.80 107.12 6.68 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C TYR B 141 " pdb=" CA TYR B 141 " pdb=" CB TYR B 141 " ideal model delta sigma weight residual 110.79 101.02 9.77 1.66e+00 3.63e-01 3.46e+01 angle pdb=" C TYR D 141 " pdb=" CA TYR D 141 " pdb=" CB TYR D 141 " ideal model delta sigma weight residual 110.79 101.18 9.61 1.66e+00 3.63e-01 3.35e+01 ... (remaining 30718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 13336 22.10 - 44.21: 578 44.21 - 66.31: 57 66.31 - 88.41: 72 88.41 - 110.52: 36 Dihedral angle restraints: 14079 sinusoidal: 6069 harmonic: 8010 Sorted by residual: dihedral pdb=" C ASP F 158 " pdb=" N ASP F 158 " pdb=" CA ASP F 158 " pdb=" CB ASP F 158 " ideal model delta harmonic sigma weight residual -122.60 -138.20 15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C ASP B 158 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " ideal model delta harmonic sigma weight residual -122.60 -137.92 15.32 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" C ASP D 158 " pdb=" N ASP D 158 " pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 14076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 3411 0.168 - 0.336: 108 0.336 - 0.504: 13 0.504 - 0.672: 2 0.672 - 0.840: 3 Chirality restraints: 3537 Sorted by residual: chirality pdb=" C1 MAN Y 4 " pdb=" O3 BMA Y 3 " pdb=" C2 MAN Y 4 " pdb=" O5 MAN Y 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.77e+03 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 1.57 0.83 2.00e-02 2.50e+03 1.73e+03 chirality pdb=" C1 MAN O 4 " pdb=" O3 BMA O 3 " pdb=" C2 MAN O 4 " pdb=" O5 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.40 1.59 0.81 2.00e-02 2.50e+03 1.65e+03 ... (remaining 3534 not shown) Planarity restraints: 3915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG N 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " -0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG S 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.338 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG X 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.117 2.00e-02 2.50e+03 ... (remaining 3912 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 972 2.71 - 3.25: 19736 3.25 - 3.80: 33860 3.80 - 4.35: 41404 4.35 - 4.90: 72331 Nonbonded interactions: 168303 Sorted by model distance: nonbonded pdb=" O3 NAG Y 1 " pdb=" O7 NAG Y 1 " model vdw 2.158 3.040 nonbonded pdb=" O3 NAG O 1 " pdb=" O7 NAG O 1 " model vdw 2.159 3.040 nonbonded pdb=" O3 NAG T 1 " pdb=" O7 NAG T 1 " model vdw 2.159 3.040 nonbonded pdb=" OG SER D 151 " pdb=" O THR D 156 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 151 " pdb=" O THR B 156 " model vdw 2.230 3.040 ... (remaining 168298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 12.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 19.090 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 34.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 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 : 14.764 110.517 8871 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 aren 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 covalent geometry : bond 0.00798 (22623) covalent geometry : angle 1.16975 (30723) SS BOND : bond 0.01537 ( 30) SS BOND : angle 2.09376 ( 60) hydrogen bonds : bond 0.17644 ( 792) hydrogen bonds : angle 7.25066 ( 2331) link_ALPHA1-3 : bond 0.03091 ( 3) link_ALPHA1-3 : angle 9.22831 ( 9) link_ALPHA1-6 : bond 0.00470 ( 3) link_ALPHA1-6 : angle 2.16631 ( 9) link_BETA1-4 : bond 0.00476 ( 24) link_BETA1-4 : angle 2.99672 ( 72) link_BETA1-6 : bond 0.00415 ( 3) link_BETA1-6 : angle 1.70213 ( 9) link_NAG-ASN : bond 0.00971 ( 15) link_NAG-ASN : angle 5.80914 ( 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 : 0.757 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: 0.1774 time to fit residues: 92.8508 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 : 0.634 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 184 HIS A 196 GLN A 250 ASN A 299 HIS A 323 ASN C 184 HIS C 250 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN E 55 GLN E 184 HIS E 299 HIS E 323 ASN 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: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.075367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.047387 restraints weight = 63668.553| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 3.43 r_work: 0.2500 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22701 Z= 0.249 Angle : 0.786 15.284 30927 Z= 0.386 Chirality : 0.049 0.295 3537 Planarity : 0.005 0.059 3900 Dihedral : 12.552 86.270 4006 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.15 % Allowed : 9.22 % Favored : 88.64 % 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 aren not related in a simple way. whole: -1.47 (0.15), residues: 2760 helix: 0.74 (0.25), residues: 423 sheet: -0.28 (0.17), residues: 909 loop : -2.05 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 87 TYR 0.017 0.002 TYR H 193 PHE 0.024 0.002 PHE I 68 TRP 0.019 0.002 TRP A 255 HIS 0.005 0.001 HIS D 111 Details of bonding type rmsd covalent geometry : bond 0.00575 (22623) covalent geometry : angle 0.75692 (30723) SS BOND : bond 0.00690 ( 30) SS BOND : angle 1.37722 ( 60) hydrogen bonds : bond 0.06373 ( 792) hydrogen bonds : angle 5.61199 ( 2331) link_ALPHA1-3 : bond 0.03930 ( 3) link_ALPHA1-3 : angle 4.25299 ( 9) link_ALPHA1-6 : bond 0.00665 ( 3) link_ALPHA1-6 : angle 1.39158 ( 9) link_BETA1-4 : bond 0.00913 ( 24) link_BETA1-4 : angle 2.98489 ( 72) link_BETA1-6 : bond 0.00625 ( 3) link_BETA1-6 : angle 1.37812 ( 9) link_NAG-ASN : bond 0.00514 ( 15) link_NAG-ASN : angle 3.52332 ( 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 226 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 175 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 211 ARG cc_start: 0.8558 (ttm170) cc_final: 0.8252 (mtp180) REVERT: C 281 ARG cc_start: 0.8890 (mtp85) cc_final: 0.8685 (mtm-85) REVERT: E 230 MET cc_start: 0.9048 (mtp) cc_final: 0.8759 (mtp) REVERT: E 239 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8533 (mt0) REVERT: G 73 ASP cc_start: 0.8303 (t0) cc_final: 0.7813 (t0) REVERT: G 114 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8420 (tp-100) REVERT: G 197 TYR cc_start: 0.6977 (m-80) cc_final: 0.6263 (m-80) REVERT: G 202 ASN cc_start: 0.7723 (t0) cc_final: 0.7421 (p0) REVERT: G 204 LYS cc_start: 0.8849 (mmmm) cc_final: 0.8559 (mmpt) REVERT: G 213 ARG cc_start: 0.8021 (ttt180) cc_final: 0.7094 (tmt-80) REVERT: H 143 ARG cc_start: 0.8782 (tmt-80) cc_final: 0.8026 (tpt170) REVERT: H 166 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8893 (mp0) REVERT: I 1 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7964 (tm-30) REVERT: I 3 GLN cc_start: 0.8103 (pm20) cc_final: 0.7777 (pm20) REVERT: I 73 ASP cc_start: 0.8024 (t0) cc_final: 0.7292 (t0) REVERT: I 76 LYS cc_start: 0.9327 (mttt) cc_final: 0.9065 (mtpp) REVERT: I 87 ARG cc_start: 0.8651 (mtm-85) cc_final: 0.8397 (mtt-85) REVERT: I 89 ASP cc_start: 0.9399 (p0) cc_final: 0.9086 (p0) REVERT: I 146 LYS cc_start: 0.8163 (tttp) cc_final: 0.7774 (tttp) REVERT: I 147 ASP cc_start: 0.8367 (m-30) cc_final: 0.8064 (m-30) REVERT: I 211 ASP cc_start: 0.6564 (m-30) cc_final: 0.6127 (t0) REVERT: I 212 LYS cc_start: 0.5784 (tppt) cc_final: 0.5114 (mmmt) REVERT: I 215 GLU cc_start: 0.6216 (pt0) cc_final: 0.5460 (tp30) REVERT: K 73 ASP cc_start: 0.8440 (t0) cc_final: 0.7926 (t0) REVERT: K 89 ASP cc_start: 0.9347 (p0) cc_final: 0.9100 (p0) REVERT: K 99 MET cc_start: 0.9404 (mmt) cc_final: 0.9026 (mmt) REVERT: K 207 ASN cc_start: 0.8859 (m110) cc_final: 0.8635 (m-40) REVERT: J 4 MET cc_start: 0.8935 (mmm) cc_final: 0.8336 (mmm) REVERT: J 108 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8590 (tptt) REVERT: J 143 ARG cc_start: 0.8541 (tmt-80) cc_final: 0.8052 (tpt90) REVERT: J 191 LYS cc_start: 0.7355 (ttmp) cc_final: 0.6830 (tmtt) REVERT: L 24 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.7786 (mtp-110) REVERT: L 70 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: L 106 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: L 108 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8326 (tptt) REVERT: L 143 ARG cc_start: 0.8720 (tmt-80) cc_final: 0.8493 (tpt-90) outliers start: 51 outliers final: 25 residues processed: 213 average time/residue: 0.1970 time to fit residues: 60.3163 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 : 0.781 ------------------------------------------------------------------------------- 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 37 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 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 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: 0.0980 chunk 135 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 228 optimal weight: 10.0000 chunk 56 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 HIS E 250 ASN G 114 GLN H 156 GLN K 114 GLN J 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.077063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.049260 restraints weight = 63129.923| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.43 r_work: 0.2548 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22701 Z= 0.124 Angle : 0.661 17.429 30927 Z= 0.319 Chirality : 0.045 0.185 3537 Planarity : 0.004 0.057 3900 Dihedral : 10.204 78.475 3999 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.31 % Allowed : 9.60 % Favored : 88.09 % 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 aren not related in a simple way. whole: -0.88 (0.16), residues: 2760 helix: 1.42 (0.25), residues: 423 sheet: -0.07 (0.17), residues: 948 loop : -1.64 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 24 TYR 0.010 0.001 TYR B 157 PHE 0.024 0.001 PHE H 140 TRP 0.012 0.001 TRP K 112 HIS 0.005 0.001 HIS L 199 Details of bonding type rmsd covalent geometry : bond 0.00257 (22623) covalent geometry : angle 0.63852 (30723) SS BOND : bond 0.00406 ( 30) SS BOND : angle 0.81763 ( 60) hydrogen bonds : bond 0.05218 ( 792) hydrogen bonds : angle 5.06539 ( 2331) link_ALPHA1-3 : bond 0.04310 ( 3) link_ALPHA1-3 : angle 4.84652 ( 9) link_ALPHA1-6 : bond 0.00907 ( 3) link_ALPHA1-6 : angle 1.16513 ( 9) link_BETA1-4 : bond 0.00812 ( 24) link_BETA1-4 : angle 2.27182 ( 72) link_BETA1-6 : bond 0.00532 ( 3) link_BETA1-6 : angle 1.13024 ( 9) link_NAG-ASN : bond 0.00143 ( 15) link_NAG-ASN : angle 2.76875 ( 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 215 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 160 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 157 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8555 (ttpp) REVERT: B 98 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9179 (tp) REVERT: C 211 ARG cc_start: 0.8523 (ttm170) cc_final: 0.8241 (mtp180) REVERT: E 157 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8499 (ttpp) REVERT: E 230 MET cc_start: 0.8992 (mtp) cc_final: 0.8710 (mtp) REVERT: G 73 ASP cc_start: 0.8293 (t0) cc_final: 0.7907 (t0) REVERT: G 114 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8171 (tp-100) REVERT: G 202 ASN cc_start: 0.7682 (t0) cc_final: 0.6927 (p0) REVERT: H 4 MET cc_start: 0.8775 (mmm) cc_final: 0.8353 (mmm) REVERT: H 24 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7704 (mtp-110) REVERT: H 104 ARG cc_start: 0.8407 (ptm160) cc_final: 0.8175 (ptm160) REVERT: H 166 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8867 (mp0) REVERT: I 1 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7966 (tm-30) REVERT: I 3 GLN cc_start: 0.8087 (pm20) cc_final: 0.7674 (pm20) REVERT: I 73 ASP cc_start: 0.8038 (t0) cc_final: 0.7401 (t0) REVERT: I 76 LYS cc_start: 0.9273 (mttt) cc_final: 0.9039 (mtpp) REVERT: I 146 LYS cc_start: 0.7992 (tttp) cc_final: 0.7603 (tttp) REVERT: I 147 ASP cc_start: 0.8437 (m-30) cc_final: 0.8094 (m-30) REVERT: I 211 ASP cc_start: 0.6424 (m-30) cc_final: 0.6030 (t0) REVERT: I 212 LYS cc_start: 0.5817 (tppt) cc_final: 0.5121 (tptt) REVERT: I 215 GLU cc_start: 0.5817 (pt0) cc_final: 0.5163 (tp30) REVERT: K 73 ASP cc_start: 0.8284 (t0) cc_final: 0.7821 (t0) REVERT: K 89 ASP cc_start: 0.9321 (p0) cc_final: 0.9098 (p0) REVERT: K 99 MET cc_start: 0.9321 (mmt) cc_final: 0.8993 (mmt) REVERT: K 207 ASN cc_start: 0.8924 (m110) cc_final: 0.8672 (m-40) REVERT: J 108 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8630 (tptt) REVERT: J 143 ARG cc_start: 0.8583 (tmt-80) cc_final: 0.8033 (tpt90) REVERT: J 191 LYS cc_start: 0.7419 (ttmp) cc_final: 0.7062 (tptt) REVERT: L 24 ARG cc_start: 0.8395 (mtp-110) cc_final: 0.7794 (mtm110) REVERT: L 70 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8480 (mm-30) REVERT: L 106 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7646 (tm-30) REVERT: L 108 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8284 (tptt) REVERT: L 143 ARG cc_start: 0.8693 (tmt-80) cc_final: 0.8130 (tpt170) outliers start: 55 outliers final: 24 residues processed: 204 average time/residue: 0.1927 time to fit residues: 56.9354 Evaluate side-chains 167 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 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 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 157 LYS 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 114 GLN Chi-restraints excluded: chain G residue 141 LEU 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: 10.0000 chunk 101 optimal weight: 3.9990 chunk 164 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 296 GLN C 231 ASN C 296 GLN E 150 ASN E 296 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.047179 restraints weight = 63483.302| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.44 r_work: 0.2495 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22701 Z= 0.217 Angle : 0.688 20.128 30927 Z= 0.335 Chirality : 0.046 0.196 3537 Planarity : 0.004 0.053 3900 Dihedral : 9.201 70.979 3992 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.90 % Allowed : 10.06 % Favored : 87.04 % 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 aren not related in a simple way. whole: -0.63 (0.16), residues: 2760 helix: 1.59 (0.25), residues: 423 sheet: 0.19 (0.17), residues: 930 loop : -1.51 (0.15), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 212 TYR 0.014 0.001 TYR C 102 PHE 0.021 0.002 PHE I 68 TRP 0.030 0.001 TRP J 149 HIS 0.006 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00505 (22623) covalent geometry : angle 0.66465 (30723) SS BOND : bond 0.00710 ( 30) SS BOND : angle 1.19121 ( 60) hydrogen bonds : bond 0.05601 ( 792) hydrogen bonds : angle 4.99087 ( 2331) link_ALPHA1-3 : bond 0.04153 ( 3) link_ALPHA1-3 : angle 4.76592 ( 9) link_ALPHA1-6 : bond 0.01018 ( 3) link_ALPHA1-6 : angle 1.25798 ( 9) link_BETA1-4 : bond 0.00729 ( 24) link_BETA1-4 : angle 2.28027 ( 72) link_BETA1-6 : bond 0.00588 ( 3) link_BETA1-6 : angle 1.08132 ( 9) link_NAG-ASN : bond 0.00290 ( 15) link_NAG-ASN : angle 2.93082 ( 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 207 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.7774 (p90) REVERT: B 98 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9172 (tp) REVERT: C 49 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9061 (mm) REVERT: C 184 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.7608 (p90) REVERT: C 211 ARG cc_start: 0.8585 (ttm170) cc_final: 0.8317 (mtp180) REVERT: E 49 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8935 (mm) REVERT: G 73 ASP cc_start: 0.8178 (t0) cc_final: 0.7836 (t0) REVERT: G 202 ASN cc_start: 0.7567 (t0) cc_final: 0.6856 (p0) REVERT: G 213 ARG cc_start: 0.7967 (ttt180) cc_final: 0.7352 (tmt-80) REVERT: H 4 MET cc_start: 0.8898 (mmm) cc_final: 0.8318 (mmm) REVERT: H 24 ARG cc_start: 0.8354 (mtp85) cc_final: 0.7765 (mtp-110) REVERT: I 73 ASP cc_start: 0.8118 (t0) cc_final: 0.7461 (t0) REVERT: I 76 LYS cc_start: 0.9329 (mttt) cc_final: 0.9101 (mtpp) REVERT: I 146 LYS cc_start: 0.7982 (tttp) cc_final: 0.7600 (tttp) REVERT: I 211 ASP cc_start: 0.6540 (m-30) cc_final: 0.6132 (t0) REVERT: I 212 LYS cc_start: 0.5848 (tppt) cc_final: 0.5139 (mmmt) REVERT: I 215 GLU cc_start: 0.5768 (pt0) cc_final: 0.5098 (tp30) REVERT: K 73 ASP cc_start: 0.8297 (t0) cc_final: 0.7899 (t0) REVERT: K 99 MET cc_start: 0.9362 (mmt) cc_final: 0.8967 (mmt) REVERT: K 207 ASN cc_start: 0.8845 (m110) cc_final: 0.8592 (m-40) REVERT: J 108 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8574 (tptt) REVERT: L 70 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8579 (mm-30) REVERT: L 106 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: L 108 LYS cc_start: 0.8980 (ttpt) cc_final: 0.8287 (tptt) outliers start: 69 outliers final: 34 residues processed: 197 average time/residue: 0.1719 time to fit residues: 49.9538 Evaluate side-chains 172 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 70 GLU 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: 0.9990 chunk 233 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 150 ASN A 296 GLN B 128 ASN C 32 HIS C 150 ASN C 183 HIS C 283 GLN C 296 GLN D 128 ASN E 231 ASN J 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.073827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.045822 restraints weight = 63537.640| |-----------------------------------------------------------------------------| r_work (start): 0.2601 rms_B_bonded: 3.44 r_work: 0.2450 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 22701 Z= 0.278 Angle : 0.726 24.326 30927 Z= 0.354 Chirality : 0.047 0.228 3537 Planarity : 0.004 0.051 3900 Dihedral : 8.756 59.776 3992 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.16 % Allowed : 10.35 % Favored : 86.49 % 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 aren not related in a simple way. whole: -0.58 (0.16), residues: 2760 helix: 1.51 (0.25), residues: 423 sheet: 0.23 (0.17), residues: 942 loop : -1.47 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 143 TYR 0.016 0.002 TYR A 102 PHE 0.024 0.002 PHE E 115 TRP 0.028 0.001 TRP J 149 HIS 0.006 0.002 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00651 (22623) covalent geometry : angle 0.70328 (30723) SS BOND : bond 0.00644 ( 30) SS BOND : angle 1.44051 ( 60) hydrogen bonds : bond 0.05981 ( 792) hydrogen bonds : angle 5.02762 ( 2331) link_ALPHA1-3 : bond 0.04139 ( 3) link_ALPHA1-3 : angle 4.94973 ( 9) link_ALPHA1-6 : bond 0.01241 ( 3) link_ALPHA1-6 : angle 1.20971 ( 9) link_BETA1-4 : bond 0.00694 ( 24) link_BETA1-4 : angle 2.15050 ( 72) link_BETA1-6 : bond 0.00609 ( 3) link_BETA1-6 : angle 1.02571 ( 9) link_NAG-ASN : bond 0.00405 ( 15) link_NAG-ASN : angle 3.00746 ( 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 213 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 138 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.9057 (OUTLIER) cc_final: 0.7801 (p90) REVERT: A 192 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8883 (tm-30) REVERT: C 49 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9060 (mm) REVERT: C 184 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.7698 (p90) REVERT: C 211 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8403 (mtp180) REVERT: E 49 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8908 (mm) REVERT: E 242 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8872 (t) REVERT: G 43 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8367 (mmtm) REVERT: G 73 ASP cc_start: 0.8136 (t0) cc_final: 0.7767 (t0) REVERT: G 202 ASN cc_start: 0.7446 (t0) cc_final: 0.6645 (p0) REVERT: G 213 ARG cc_start: 0.7866 (ttt180) cc_final: 0.7147 (tmt-80) REVERT: H 4 MET cc_start: 0.8931 (mmm) cc_final: 0.8297 (mmm) REVERT: H 24 ARG cc_start: 0.8343 (mtp85) cc_final: 0.7748 (mtp-110) REVERT: I 73 ASP cc_start: 0.8097 (t0) cc_final: 0.7433 (t0) REVERT: I 76 LYS cc_start: 0.9367 (mttt) cc_final: 0.9143 (mtpp) REVERT: I 146 LYS cc_start: 0.7938 (tttp) cc_final: 0.7592 (tttp) REVERT: I 147 ASP cc_start: 0.8438 (m-30) cc_final: 0.8175 (m-30) REVERT: I 212 LYS cc_start: 0.5979 (tppt) cc_final: 0.5199 (mmmt) REVERT: I 215 GLU cc_start: 0.5233 (pt0) cc_final: 0.4998 (tp30) REVERT: K 73 ASP cc_start: 0.8192 (t0) cc_final: 0.7727 (t0) REVERT: K 99 MET cc_start: 0.9364 (mmt) cc_final: 0.8955 (mmt) REVERT: K 207 ASN cc_start: 0.8879 (m110) cc_final: 0.8549 (p0) REVERT: L 24 ARG cc_start: 0.8518 (mtp-110) cc_final: 0.8088 (mtp-110) REVERT: L 70 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8741 (mm-30) REVERT: L 79 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: L 106 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: L 108 LYS cc_start: 0.8970 (ttpt) cc_final: 0.8291 (tptt) outliers start: 75 outliers final: 49 residues processed: 201 average time/residue: 0.1739 time to fit residues: 51.4051 Evaluate side-chains 185 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 128 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 184 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 163 SER Chi-restraints excluded: chain C residue 5 ASP Chi-restraints excluded: chain C residue 30 VAL 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 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 30 VAL 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 E residue 296 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 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 48 ILE 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 79 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 70 GLU Chi-restraints excluded: chain L 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 1 optimal weight: 7.9990 chunk 175 optimal weight: 0.6980 chunk 233 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 chunk 201 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN I 158 ASN J 37 GLN L 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.075672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.047793 restraints weight = 63036.723| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.42 r_work: 0.2502 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22701 Z= 0.134 Angle : 0.647 23.975 30927 Z= 0.307 Chirality : 0.044 0.241 3537 Planarity : 0.004 0.050 3900 Dihedral : 8.225 59.898 3992 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.82 % Allowed : 11.03 % 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 aren not related in a simple way. whole: -0.28 (0.16), residues: 2760 helix: 1.92 (0.26), residues: 423 sheet: 0.42 (0.17), residues: 933 loop : -1.31 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 143 TYR 0.014 0.001 TYR I 80 PHE 0.015 0.001 PHE H 140 TRP 0.016 0.001 TRP J 149 HIS 0.004 0.001 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00296 (22623) covalent geometry : angle 0.62379 (30723) SS BOND : bond 0.00435 ( 30) SS BOND : angle 1.51751 ( 60) hydrogen bonds : bond 0.05088 ( 792) hydrogen bonds : angle 4.74372 ( 2331) link_ALPHA1-3 : bond 0.04028 ( 3) link_ALPHA1-3 : angle 4.90465 ( 9) link_ALPHA1-6 : bond 0.01111 ( 3) link_ALPHA1-6 : angle 1.51751 ( 9) link_BETA1-4 : bond 0.00709 ( 24) link_BETA1-4 : angle 2.07666 ( 72) link_BETA1-6 : bond 0.00575 ( 3) link_BETA1-6 : angle 1.03719 ( 9) link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 2.56237 ( 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 204 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 137 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.7755 (p90) REVERT: A 192 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8820 (tm-30) REVERT: C 184 HIS cc_start: 0.8718 (OUTLIER) cc_final: 0.7516 (p90) REVERT: C 211 ARG cc_start: 0.8615 (ttm170) cc_final: 0.8377 (mtp180) REVERT: G 43 LYS cc_start: 0.8665 (mmtp) cc_final: 0.8292 (mmtm) REVERT: G 73 ASP cc_start: 0.8112 (t0) cc_final: 0.7654 (t0) REVERT: H 4 MET cc_start: 0.8851 (mmm) cc_final: 0.8335 (mmm) REVERT: H 24 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7171 (mtp85) REVERT: H 79 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: H 104 ARG cc_start: 0.8580 (ptm-80) cc_final: 0.7779 (ptt90) REVERT: I 3 GLN cc_start: 0.8020 (pm20) cc_final: 0.7695 (pm20) REVERT: I 73 ASP cc_start: 0.8058 (t0) cc_final: 0.7399 (t0) REVERT: I 76 LYS cc_start: 0.9347 (mttt) cc_final: 0.9124 (mtpp) REVERT: I 146 LYS cc_start: 0.7963 (tttp) cc_final: 0.7686 (tttp) REVERT: I 197 TYR cc_start: 0.7282 (m-80) cc_final: 0.7031 (m-80) REVERT: I 211 ASP cc_start: 0.6656 (m-30) cc_final: 0.6338 (t0) REVERT: I 215 GLU cc_start: 0.5669 (pt0) cc_final: 0.5099 (tp30) REVERT: K 73 ASP cc_start: 0.8192 (t0) cc_final: 0.7745 (t0) REVERT: K 99 MET cc_start: 0.9332 (mmt) cc_final: 0.8952 (mmt) REVERT: K 207 ASN cc_start: 0.8871 (m110) cc_final: 0.8634 (m-40) REVERT: L 24 ARG cc_start: 0.8441 (mtp-110) cc_final: 0.7927 (mtp-110) REVERT: L 70 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8615 (mm-30) REVERT: L 106 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: L 108 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8338 (tptt) REVERT: L 109 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7475 (ptm-80) outliers start: 67 outliers final: 38 residues processed: 193 average time/residue: 0.1889 time to fit residues: 52.6368 Evaluate side-chains 174 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 130 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 98 LEU 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 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 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 163 SER 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 79 GLN Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain H residue 170 LYS Chi-restraints excluded: chain H residue 190 HIS Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 109 ARG 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: 0.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 272 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 chunk 265 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 296 GLN C 283 GLN C 296 GLN E 296 GLN F 128 ASN J 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.047423 restraints weight = 63209.265| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.44 r_work: 0.2494 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22701 Z= 0.164 Angle : 0.647 24.219 30927 Z= 0.307 Chirality : 0.044 0.229 3537 Planarity : 0.004 0.052 3900 Dihedral : 8.026 56.912 3992 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.86 % Allowed : 11.11 % Favored : 86.03 % 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 aren not related in a simple way. whole: -0.18 (0.16), residues: 2760 helix: 2.00 (0.26), residues: 423 sheet: 0.51 (0.18), residues: 930 loop : -1.28 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 100 TYR 0.013 0.001 TYR K 197 PHE 0.015 0.001 PHE C 115 TRP 0.025 0.001 TRP J 149 HIS 0.004 0.001 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00377 (22623) covalent geometry : angle 0.62446 (30723) SS BOND : bond 0.00452 ( 30) SS BOND : angle 1.35322 ( 60) hydrogen bonds : bond 0.05133 ( 792) hydrogen bonds : angle 4.67859 ( 2331) link_ALPHA1-3 : bond 0.03976 ( 3) link_ALPHA1-3 : angle 4.99015 ( 9) link_ALPHA1-6 : bond 0.01078 ( 3) link_ALPHA1-6 : angle 1.60087 ( 9) link_BETA1-4 : bond 0.00672 ( 24) link_BETA1-4 : angle 2.08420 ( 72) link_BETA1-6 : bond 0.00591 ( 3) link_BETA1-6 : angle 1.04407 ( 9) link_NAG-ASN : bond 0.00185 ( 15) link_NAG-ASN : angle 2.53336 ( 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 200 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 132 time to evaluate : 0.544 Fit side-chains REVERT: A 184 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.7769 (p90) REVERT: A 192 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8819 (tm-30) REVERT: C 184 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.7590 (p90) REVERT: C 211 ARG cc_start: 0.8630 (ttm170) cc_final: 0.8405 (mtp180) REVERT: E 242 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8904 (t) REVERT: G 43 LYS cc_start: 0.8661 (mmtp) cc_final: 0.8276 (mmtm) REVERT: G 73 ASP cc_start: 0.8127 (t0) cc_final: 0.7648 (t0) REVERT: H 4 MET cc_start: 0.8889 (mmm) cc_final: 0.8326 (mmm) REVERT: H 24 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7123 (mtp85) REVERT: H 79 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: H 104 ARG cc_start: 0.8564 (ptm-80) cc_final: 0.7766 (ptt90) REVERT: I 3 GLN cc_start: 0.8019 (pm20) cc_final: 0.7686 (pm20) REVERT: I 73 ASP cc_start: 0.8107 (t0) cc_final: 0.7443 (t0) REVERT: I 76 LYS cc_start: 0.9338 (mttt) cc_final: 0.9123 (mtpp) REVERT: I 146 LYS cc_start: 0.7948 (tttp) cc_final: 0.7596 (tttp) REVERT: I 147 ASP cc_start: 0.8485 (m-30) cc_final: 0.8210 (m-30) REVERT: I 197 TYR cc_start: 0.7299 (m-80) cc_final: 0.7041 (m-80) REVERT: I 211 ASP cc_start: 0.6730 (m-30) cc_final: 0.6331 (t0) REVERT: I 215 GLU cc_start: 0.5674 (pt0) cc_final: 0.5092 (tp30) REVERT: K 73 ASP cc_start: 0.8196 (t0) cc_final: 0.7728 (t0) REVERT: K 99 MET cc_start: 0.9341 (mmt) cc_final: 0.8915 (mmt) REVERT: K 207 ASN cc_start: 0.8867 (m110) cc_final: 0.8625 (m-40) REVERT: J 143 ARG cc_start: 0.8967 (tpt-90) cc_final: 0.8665 (tpt170) REVERT: L 24 ARG cc_start: 0.8455 (mtp-110) cc_final: 0.7936 (mtp-110) REVERT: L 70 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8643 (mm-30) REVERT: L 106 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: L 108 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8391 (tptt) REVERT: L 109 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7460 (ptm-80) outliers start: 68 outliers final: 44 residues processed: 190 average time/residue: 0.1724 time to fit residues: 48.3544 Evaluate side-chains 177 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 166 SER Chi-restraints excluded: chain B residue 173 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 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 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 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 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 109 ARG Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 190 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 74 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 259 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 166 optimal weight: 0.1980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN E 296 GLN J 37 GLN L 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.075903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.048058 restraints weight = 62820.968| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.41 r_work: 0.2515 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22701 Z= 0.135 Angle : 0.630 23.962 30927 Z= 0.298 Chirality : 0.044 0.212 3537 Planarity : 0.004 0.053 3900 Dihedral : 7.821 59.963 3992 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.53 % Allowed : 11.74 % 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 aren not related in a simple way. whole: -0.11 (0.16), residues: 2760 helix: 2.08 (0.26), residues: 426 sheet: 0.64 (0.18), residues: 915 loop : -1.28 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 100 TYR 0.013 0.001 TYR K 197 PHE 0.012 0.001 PHE H 140 TRP 0.031 0.001 TRP J 149 HIS 0.004 0.001 HIS K 203 Details of bonding type rmsd covalent geometry : bond 0.00302 (22623) covalent geometry : angle 0.60744 (30723) SS BOND : bond 0.00406 ( 30) SS BOND : angle 1.40210 ( 60) hydrogen bonds : bond 0.04892 ( 792) hydrogen bonds : angle 4.57856 ( 2331) link_ALPHA1-3 : bond 0.03942 ( 3) link_ALPHA1-3 : angle 5.03668 ( 9) link_ALPHA1-6 : bond 0.01073 ( 3) link_ALPHA1-6 : angle 1.77672 ( 9) link_BETA1-4 : bond 0.00694 ( 24) link_BETA1-4 : angle 2.07003 ( 72) link_BETA1-6 : bond 0.00592 ( 3) link_BETA1-6 : angle 1.05306 ( 9) link_NAG-ASN : bond 0.00145 ( 15) link_NAG-ASN : angle 2.37442 ( 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 191 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8793 (OUTLIER) cc_final: 0.7759 (p90) REVERT: A 192 GLN cc_start: 0.9061 (tm-30) cc_final: 0.8798 (tm-30) REVERT: C 184 HIS cc_start: 0.8635 (OUTLIER) cc_final: 0.7569 (p90) REVERT: C 211 ARG cc_start: 0.8607 (ttm170) cc_final: 0.8401 (mtp180) REVERT: G 43 LYS cc_start: 0.8682 (mmtp) cc_final: 0.8360 (mmtm) REVERT: G 73 ASP cc_start: 0.8134 (t0) cc_final: 0.7700 (t0) REVERT: H 4 MET cc_start: 0.8859 (mmm) cc_final: 0.8317 (mmm) REVERT: H 24 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7136 (mtp85) REVERT: H 79 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7021 (mp10) REVERT: H 104 ARG cc_start: 0.8546 (ptm-80) cc_final: 0.7749 (ptt90) REVERT: I 73 ASP cc_start: 0.8124 (t0) cc_final: 0.7472 (t0) REVERT: I 76 LYS cc_start: 0.9340 (mttt) cc_final: 0.9136 (mtpp) REVERT: I 146 LYS cc_start: 0.7926 (tttp) cc_final: 0.7587 (tttp) REVERT: I 147 ASP cc_start: 0.8498 (m-30) cc_final: 0.8209 (m-30) REVERT: I 197 TYR cc_start: 0.7283 (m-80) cc_final: 0.7025 (m-80) REVERT: I 211 ASP cc_start: 0.6715 (m-30) cc_final: 0.6322 (t0) REVERT: I 215 GLU cc_start: 0.5694 (pt0) cc_final: 0.5194 (tp30) REVERT: K 6 GLU cc_start: 0.7772 (pm20) cc_final: 0.7442 (pm20) REVERT: K 73 ASP cc_start: 0.8194 (t0) cc_final: 0.7750 (t0) REVERT: K 99 MET cc_start: 0.9330 (mmt) cc_final: 0.8919 (mmt) REVERT: K 207 ASN cc_start: 0.8861 (m110) cc_final: 0.8617 (m-40) REVERT: J 143 ARG cc_start: 0.8954 (tpt-90) cc_final: 0.8617 (tpt170) REVERT: L 24 ARG cc_start: 0.8451 (mtp-110) cc_final: 0.7790 (mtp-110) REVERT: L 70 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8743 (mm-30) REVERT: L 106 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: L 108 LYS cc_start: 0.9070 (ttpt) cc_final: 0.8405 (tptt) outliers start: 60 outliers final: 39 residues processed: 181 average time/residue: 0.1929 time to fit residues: 51.3895 Evaluate side-chains 169 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 98 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain C residue 20 VAL 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 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 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 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 141 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 187 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 184 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 224 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN E 183 HIS E 296 GLN H 37 GLN J 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.073432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.045521 restraints weight = 63571.677| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 3.43 r_work: 0.2438 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 22701 Z= 0.337 Angle : 0.752 25.767 30927 Z= 0.366 Chirality : 0.048 0.221 3537 Planarity : 0.005 0.052 3900 Dihedral : 7.896 56.968 3992 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.57 % Allowed : 11.91 % Favored : 85.52 % 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 aren not related in a simple way. whole: -0.35 (0.16), residues: 2760 helix: 1.68 (0.25), residues: 426 sheet: 0.51 (0.18), residues: 909 loop : -1.38 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 101 TYR 0.016 0.002 TYR H 193 PHE 0.027 0.002 PHE E 115 TRP 0.072 0.002 TRP J 149 HIS 0.007 0.002 HIS C 32 Details of bonding type rmsd covalent geometry : bond 0.00795 (22623) covalent geometry : angle 0.72905 (30723) SS BOND : bond 0.00675 ( 30) SS BOND : angle 1.77989 ( 60) hydrogen bonds : bond 0.06045 ( 792) hydrogen bonds : angle 4.90388 ( 2331) link_ALPHA1-3 : bond 0.03849 ( 3) link_ALPHA1-3 : angle 5.10085 ( 9) link_ALPHA1-6 : bond 0.01232 ( 3) link_ALPHA1-6 : angle 1.67122 ( 9) link_BETA1-4 : bond 0.00671 ( 24) link_BETA1-4 : angle 2.15880 ( 72) link_BETA1-6 : bond 0.00631 ( 3) link_BETA1-6 : angle 1.03558 ( 9) link_NAG-ASN : bond 0.00492 ( 15) link_NAG-ASN : angle 2.80173 ( 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 187 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 126 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 HIS cc_start: 0.9095 (OUTLIER) cc_final: 0.7811 (p90) REVERT: A 192 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8867 (tm-30) REVERT: C 184 HIS cc_start: 0.8917 (OUTLIER) cc_final: 0.7777 (p90) REVERT: C 211 ARG cc_start: 0.8691 (ttm170) cc_final: 0.8445 (mtp180) REVERT: E 242 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8888 (t) REVERT: E 296 GLN cc_start: 0.9315 (OUTLIER) cc_final: 0.9109 (tm130) REVERT: G 43 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8493 (mmtm) REVERT: G 73 ASP cc_start: 0.8219 (t0) cc_final: 0.7766 (t0) REVERT: H 4 MET cc_start: 0.9027 (mmm) cc_final: 0.8232 (mmm) REVERT: H 24 ARG cc_start: 0.8433 (mtp85) cc_final: 0.8004 (mtp-110) REVERT: H 79 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: I 43 LYS cc_start: 0.9022 (mmtp) cc_final: 0.8610 (mmtm) REVERT: I 73 ASP cc_start: 0.8113 (t0) cc_final: 0.7451 (t0) REVERT: I 146 LYS cc_start: 0.7979 (tttp) cc_final: 0.7625 (tttp) REVERT: I 147 ASP cc_start: 0.8523 (m-30) cc_final: 0.8240 (m-30) REVERT: I 197 TYR cc_start: 0.7342 (m-80) cc_final: 0.7044 (m-80) REVERT: K 73 ASP cc_start: 0.8215 (t0) cc_final: 0.7804 (t0) REVERT: K 99 MET cc_start: 0.9355 (mmt) cc_final: 0.8927 (mmt) REVERT: K 126 LYS cc_start: 0.8396 (tptp) cc_final: 0.7881 (tmtt) REVERT: K 207 ASN cc_start: 0.8877 (m110) cc_final: 0.8599 (p0) REVERT: L 24 ARG cc_start: 0.8536 (mtp-110) cc_final: 0.8119 (mtp-110) REVERT: L 70 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8708 (mm-30) REVERT: L 106 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: L 108 LYS cc_start: 0.9097 (ttpt) cc_final: 0.8492 (tptt) outliers start: 61 outliers final: 42 residues processed: 178 average time/residue: 0.1814 time to fit residues: 48.2375 Evaluate side-chains 172 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 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 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 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 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 E residue 296 GLN Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 18 ILE 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 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 79 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 70 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 105 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN E 296 GLN H 37 GLN K 3 GLN J 37 GLN L 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.047224 restraints weight = 63073.530| |-----------------------------------------------------------------------------| r_work (start): 0.2637 rms_B_bonded: 3.42 r_work: 0.2487 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22701 Z= 0.148 Angle : 0.662 25.901 30927 Z= 0.314 Chirality : 0.044 0.210 3537 Planarity : 0.004 0.050 3900 Dihedral : 7.613 59.966 3992 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.36 % Allowed : 12.29 % Favored : 85.35 % 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 aren not related in a simple way. whole: -0.16 (0.16), residues: 2760 helix: 1.89 (0.26), residues: 426 sheet: 0.63 (0.18), residues: 909 loop : -1.28 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 101 TYR 0.013 0.001 TYR K 197 PHE 0.013 0.001 PHE C 115 TRP 0.058 0.001 TRP J 149 HIS 0.005 0.001 HIS K 203 Details of bonding type rmsd covalent geometry : bond 0.00337 (22623) covalent geometry : angle 0.63959 (30723) SS BOND : bond 0.00427 ( 30) SS BOND : angle 1.49758 ( 60) hydrogen bonds : bond 0.05229 ( 792) hydrogen bonds : angle 4.67082 ( 2331) link_ALPHA1-3 : bond 0.03752 ( 3) link_ALPHA1-3 : angle 5.13010 ( 9) link_ALPHA1-6 : bond 0.01009 ( 3) link_ALPHA1-6 : angle 1.84699 ( 9) link_BETA1-4 : bond 0.00704 ( 24) link_BETA1-4 : angle 2.08181 ( 72) link_BETA1-6 : bond 0.00589 ( 3) link_BETA1-6 : angle 1.06933 ( 9) link_NAG-ASN : bond 0.00188 ( 15) link_NAG-ASN : angle 2.41167 ( 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 186 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 130 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 184 HIS cc_start: 0.8953 (OUTLIER) cc_final: 0.7778 (p90) REVERT: A 192 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8839 (tm-30) REVERT: C 184 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.7662 (p90) REVERT: C 211 ARG cc_start: 0.8626 (ttm170) cc_final: 0.8387 (mtp180) REVERT: E 242 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8895 (t) REVERT: G 43 LYS cc_start: 0.8723 (mmtp) cc_final: 0.8470 (mmtp) REVERT: G 73 ASP cc_start: 0.8156 (t0) cc_final: 0.7683 (t0) REVERT: H 4 MET cc_start: 0.8901 (mmm) cc_final: 0.8296 (mmm) REVERT: H 24 ARG cc_start: 0.8288 (mtp85) cc_final: 0.7673 (mtp-110) REVERT: H 104 ARG cc_start: 0.8601 (ptm-80) cc_final: 0.7885 (ptt90) REVERT: I 73 ASP cc_start: 0.8186 (t0) cc_final: 0.7670 (t0) REVERT: I 146 LYS cc_start: 0.7941 (tttp) cc_final: 0.7601 (tttp) REVERT: I 147 ASP cc_start: 0.8531 (m-30) cc_final: 0.8251 (m-30) REVERT: I 197 TYR cc_start: 0.7284 (m-80) cc_final: 0.6980 (m-80) REVERT: K 6 GLU cc_start: 0.7677 (pm20) cc_final: 0.7413 (pm20) REVERT: K 73 ASP cc_start: 0.8106 (t0) cc_final: 0.7654 (t0) REVERT: K 99 MET cc_start: 0.9335 (mmt) cc_final: 0.8926 (mmt) REVERT: K 207 ASN cc_start: 0.8881 (m110) cc_final: 0.8659 (m-40) REVERT: L 24 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.7989 (mtp-110) REVERT: L 70 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8738 (mm-30) REVERT: L 108 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8437 (tptt) outliers start: 56 outliers final: 44 residues processed: 176 average time/residue: 0.1876 time to fit residues: 48.7426 Evaluate side-chains 173 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 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 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 166 SER Chi-restraints excluded: chain C residue 20 VAL 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 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 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 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 79 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 200 ASN Chi-restraints excluded: chain J residue 37 GLN Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 187 TYR Chi-restraints excluded: chain L residue 190 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 190 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 213 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 174 optimal weight: 0.5980 chunk 269 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 158 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN C 296 GLN E 296 GLN H 37 GLN 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 = 0.3332 r_free = 0.3332 target = 0.076112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.048265 restraints weight = 62737.494| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 3.42 r_work: 0.2521 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22701 Z= 0.115 Angle : 0.641 25.067 30927 Z= 0.302 Chirality : 0.043 0.196 3537 Planarity : 0.004 0.050 3900 Dihedral : 7.399 59.452 3992 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.27 % Allowed : 12.58 % Favored : 85.14 % 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 aren not related in a simple way. whole: -0.02 (0.16), residues: 2760 helix: 2.09 (0.26), residues: 426 sheet: 0.66 (0.18), residues: 927 loop : -1.20 (0.16), residues: 1407 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 0.011 0.001 PHE H 140 TRP 0.054 0.001 TRP J 149 HIS 0.004 0.001 HIS K 203 Details of bonding type rmsd covalent geometry : bond 0.00247 (22623) covalent geometry : angle 0.61898 (30723) SS BOND : bond 0.00356 ( 30) SS BOND : angle 1.32321 ( 60) hydrogen bonds : bond 0.04801 ( 792) hydrogen bonds : angle 4.52256 ( 2331) link_ALPHA1-3 : bond 0.03761 ( 3) link_ALPHA1-3 : angle 5.37154 ( 9) link_ALPHA1-6 : bond 0.00864 ( 3) link_ALPHA1-6 : angle 1.84516 ( 9) link_BETA1-4 : bond 0.00712 ( 24) link_BETA1-4 : angle 2.05232 ( 72) link_BETA1-6 : bond 0.00579 ( 3) link_BETA1-6 : angle 1.09318 ( 9) link_NAG-ASN : bond 0.00151 ( 15) link_NAG-ASN : angle 2.20074 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5361.67 seconds wall clock time: 92 minutes 45.70 seconds (5565.70 seconds total)