Starting phenix.real_space_refine on Sun Aug 9 05:22:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pdn_17615/08_2026/8pdn_17615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdn_17615/08_2026/8pdn_17615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2026/8pdn_17615.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2026/8pdn_17615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2026/8pdn_17615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2026/8pdn_17615.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2026/8pdn_17615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2026/8pdn_17615.cif" } resolution = 4.7 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= 0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 84 5.49 5 S 132 5.16 5 C 20700 2.51 5 N 5724 2.21 5 O 6588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33228 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "C" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "E" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "F" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "G" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "H" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "I" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "J" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "K" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "L" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2629 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 11, 'TRANS': 327} Chain breaks: 1 Chain: "a" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "b" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "c" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "d" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "e" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "f" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "g" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "h" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "i" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "j" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "k" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "l" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 6.58, per 1000 atoms: 0.20 Number of scatterers: 33228 At special positions: 0 Unit cell: (126, 201.6, 202.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 84 15.00 O 6588 8.00 N 5724 7.00 C 20700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 31692 O5' C b 400 .*. O " rejected from bonding due to valence issues. Atom "ATOM 31972 O5' C d 400 .*. O " rejected from bonding due to valence issues. Atom "ATOM 31832 O5' C c 400 .*. O " rejected from bonding due to valence issues. Atom "ATOM 32112 O5' C e 400 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.7 seconds 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7560 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 24 sheets defined 69.9% alpha, 2.4% beta 0 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 5.17 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 360 Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 141 Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 175 through 191 removed outlier: 4.143A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 344 through 360 Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 141 Processing helix chain 'C' and resid 156 through 170 Processing helix chain 'C' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 296 removed outlier: 4.684A pdb=" N LYS C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 120 through 141 Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 175 through 191 removed outlier: 4.143A pdb=" N ARG D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG D 260 " --> pdb=" O GLN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 296 removed outlier: 4.682A pdb=" N LYS D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 300 removed outlier: 3.822A pdb=" N GLY D 300 " --> pdb=" O PRO D 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 318 through 332 Processing helix chain 'D' and resid 344 through 360 Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.895A pdb=" N LEU E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 141 Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 175 through 191 removed outlier: 4.144A pdb=" N ARG E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.847A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 344 through 360 Processing helix chain 'F' and resid 11 through 20 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU F 46 " --> pdb=" O GLN F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 75 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 120 through 141 Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 175 through 191 removed outlier: 4.143A pdb=" N ARG F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 218 through 233 removed outlier: 3.845A pdb=" N SER F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 251 Processing helix chain 'F' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG F 260 " --> pdb=" O GLN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 275 through 296 removed outlier: 4.682A pdb=" N LYS F 283 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY F 300 " --> pdb=" O PRO F 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 318 through 332 Processing helix chain 'F' and resid 344 through 360 Processing helix chain 'G' and resid 11 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.894A pdb=" N LEU G 46 " --> pdb=" O GLN G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 141 Processing helix chain 'G' and resid 156 through 170 Processing helix chain 'G' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.845A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 251 Processing helix chain 'G' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 360 Processing helix chain 'H' and resid 11 through 20 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU H 46 " --> pdb=" O GLN H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 120 through 141 Processing helix chain 'H' and resid 156 through 170 Processing helix chain 'H' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 198 Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER H 222 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 251 Processing helix chain 'H' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG H 260 " --> pdb=" O GLN H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 274 Processing helix chain 'H' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS H 283 " --> pdb=" O GLN H 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN H 284 " --> pdb=" O ALA H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY H 300 " --> pdb=" O PRO H 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 297 through 300' Processing helix chain 'H' and resid 318 through 332 Processing helix chain 'H' and resid 344 through 360 Processing helix chain 'I' and resid 11 through 20 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 51 removed outlier: 3.895A pdb=" N LEU I 46 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 141 Processing helix chain 'I' and resid 156 through 170 Processing helix chain 'I' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 251 Processing helix chain 'I' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG I 260 " --> pdb=" O GLN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 274 Processing helix chain 'I' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS I 283 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 297 through 300' Processing helix chain 'I' and resid 318 through 332 Processing helix chain 'I' and resid 344 through 360 Processing helix chain 'J' and resid 11 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 51 removed outlier: 3.895A pdb=" N LEU J 46 " --> pdb=" O GLN J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 141 Processing helix chain 'J' and resid 156 through 170 Processing helix chain 'J' and resid 175 through 191 removed outlier: 4.141A pdb=" N ARG J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 218 through 233 removed outlier: 3.846A pdb=" N SER J 222 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 251 Processing helix chain 'J' and resid 256 through 269 removed outlier: 3.594A pdb=" N ARG J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 274 Processing helix chain 'J' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS J 283 " --> pdb=" O GLN J 279 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN J 284 " --> pdb=" O ALA J 280 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 300 removed outlier: 3.820A pdb=" N GLY J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 297 through 300' Processing helix chain 'J' and resid 318 through 332 Processing helix chain 'J' and resid 344 through 360 Processing helix chain 'K' and resid 11 through 20 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.896A pdb=" N LEU K 46 " --> pdb=" O GLN K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 141 Processing helix chain 'K' and resid 156 through 170 Processing helix chain 'K' and resid 175 through 191 removed outlier: 4.142A pdb=" N ARG K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 198 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 218 through 233 removed outlier: 3.845A pdb=" N SER K 222 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 251 Processing helix chain 'K' and resid 256 through 269 removed outlier: 3.592A pdb=" N ARG K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS K 283 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N GLN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY K 300 " --> pdb=" O PRO K 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 318 through 332 Processing helix chain 'K' and resid 344 through 360 Processing helix chain 'L' and resid 11 through 20 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 40 through 51 removed outlier: 3.895A pdb=" N LEU L 46 " --> pdb=" O GLN L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 75 Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 120 through 141 Processing helix chain 'L' and resid 156 through 170 Processing helix chain 'L' and resid 175 through 191 removed outlier: 4.143A pdb=" N ARG L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 198 Processing helix chain 'L' and resid 202 through 217 Processing helix chain 'L' and resid 218 through 233 removed outlier: 3.845A pdb=" N SER L 222 " --> pdb=" O VAL L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 251 Processing helix chain 'L' and resid 256 through 269 removed outlier: 3.593A pdb=" N ARG L 260 " --> pdb=" O GLN L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 275 through 296 removed outlier: 4.683A pdb=" N LYS L 283 " --> pdb=" O GLN L 279 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLN L 284 " --> pdb=" O ALA L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 297 through 300 removed outlier: 3.821A pdb=" N GLY L 300 " --> pdb=" O PRO L 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 297 through 300' Processing helix chain 'L' and resid 318 through 332 Processing helix chain 'L' and resid 344 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR B 33 " --> pdb=" O VAL B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG B 96 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG C 96 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR D 33 " --> pdb=" O VAL D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 98 removed outlier: 3.696A pdb=" N ARG D 96 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR E 33 " --> pdb=" O VAL E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG E 96 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR F 33 " --> pdb=" O VAL F 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 96 through 98 removed outlier: 3.694A pdb=" N ARG F 96 " --> pdb=" O ASP F 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 96 through 98 removed outlier: 3.694A pdb=" N ARG G 96 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.300A pdb=" N THR H 33 " --> pdb=" O VAL H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG H 96 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR I 33 " --> pdb=" O VAL I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG I 96 " --> pdb=" O ASP I 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR J 33 " --> pdb=" O VAL J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'J' and resid 96 through 98 removed outlier: 3.696A pdb=" N ARG J 96 " --> pdb=" O ASP J 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.298A pdb=" N THR K 33 " --> pdb=" O VAL K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 96 through 98 removed outlier: 3.696A pdb=" N ARG K 96 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 32 through 34 removed outlier: 6.299A pdb=" N THR L 33 " --> pdb=" O VAL L 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 96 through 98 removed outlier: 3.695A pdb=" N ARG L 96 " --> pdb=" O ASP L 115 " (cutoff:3.500A) 1969 hydrogen bonds defined for protein. 5799 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10673 1.34 - 1.46: 5006 1.46 - 1.57: 17825 1.57 - 1.69: 156 1.69 - 1.81: 228 Bond restraints: 33888 Sorted by residual: bond pdb=" C VAL K 35 " pdb=" N THR K 36 " ideal model delta sigma weight residual 1.331 1.302 0.028 1.24e-02 6.50e+03 5.21e+00 bond pdb=" C VAL I 35 " pdb=" N THR I 36 " ideal model delta sigma weight residual 1.331 1.303 0.028 1.24e-02 6.50e+03 5.06e+00 bond pdb=" C VAL A 35 " pdb=" N THR A 36 " ideal model delta sigma weight residual 1.331 1.303 0.028 1.24e-02 6.50e+03 4.96e+00 bond pdb=" C VAL H 35 " pdb=" N THR H 36 " ideal model delta sigma weight residual 1.331 1.303 0.028 1.24e-02 6.50e+03 4.94e+00 bond pdb=" C VAL B 35 " pdb=" N THR B 36 " ideal model delta sigma weight residual 1.331 1.303 0.027 1.24e-02 6.50e+03 4.90e+00 ... (remaining 33883 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 43701 1.45 - 2.90: 2089 2.90 - 4.35: 275 4.35 - 5.79: 15 5.79 - 7.24: 24 Bond angle restraints: 46104 Sorted by residual: angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.60 115.36 7.24 1.56e+00 4.11e-01 2.16e+01 angle pdb=" C LEU B 52 " pdb=" N TYR B 53 " pdb=" CA TYR B 53 " ideal model delta sigma weight residual 122.60 115.43 7.17 1.56e+00 4.11e-01 2.12e+01 angle pdb=" C LEU L 52 " pdb=" N TYR L 53 " pdb=" CA TYR L 53 " ideal model delta sigma weight residual 122.60 115.44 7.16 1.56e+00 4.11e-01 2.11e+01 angle pdb=" C LEU C 52 " pdb=" N TYR C 53 " pdb=" CA TYR C 53 " ideal model delta sigma weight residual 122.60 115.45 7.15 1.56e+00 4.11e-01 2.10e+01 angle pdb=" C LEU K 52 " pdb=" N TYR K 53 " pdb=" CA TYR K 53 " ideal model delta sigma weight residual 122.60 115.45 7.15 1.56e+00 4.11e-01 2.10e+01 ... (remaining 46099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 18347 17.53 - 35.07: 1897 35.07 - 52.60: 324 52.60 - 70.13: 168 70.13 - 87.67: 132 Dihedral angle restraints: 20868 sinusoidal: 9084 harmonic: 11784 Sorted by residual: dihedral pdb=" C4' C d 403 " pdb=" C3' C d 403 " pdb=" C2' C d 403 " pdb=" C1' C d 403 " ideal model delta sinusoidal sigma weight residual 36.34 -33.17 69.52 1 3.10e+00 1.04e-01 6.49e+02 dihedral pdb=" C4' C c 403 " pdb=" C3' C c 403 " pdb=" C2' C c 403 " pdb=" C1' C c 403 " ideal model delta sinusoidal sigma weight residual 36.34 -33.16 69.50 1 3.10e+00 1.04e-01 6.49e+02 dihedral pdb=" C4' C e 403 " pdb=" C3' C e 403 " pdb=" C2' C e 403 " pdb=" C1' C e 403 " ideal model delta sinusoidal sigma weight residual 36.34 -33.15 69.49 1 3.10e+00 1.04e-01 6.49e+02 ... (remaining 20865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4285 0.054 - 0.108: 894 0.108 - 0.162: 137 0.162 - 0.216: 73 0.216 - 0.271: 47 Chirality restraints: 5436 Sorted by residual: chirality pdb=" C2' C k 403 " pdb=" C3' C k 403 " pdb=" O2' C k 403 " pdb=" C1' C k 403 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2' C h 403 " pdb=" C3' C h 403 " pdb=" O2' C h 403 " pdb=" C1' C h 403 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2' C g 403 " pdb=" C3' C g 403 " pdb=" O2' C g 403 " pdb=" C1' C g 403 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 5433 not shown) Planarity restraints: 5580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 198 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO L 199 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 199 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 198 " 0.033 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO B 199 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR H 198 " -0.033 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO H 199 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO H 199 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 199 " -0.028 5.00e-02 4.00e+02 ... (remaining 5577 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.77: 19 1.77 - 2.55: 361 2.55 - 3.33: 42332 3.33 - 4.12: 83623 4.12 - 4.90: 155072 Warning: very small nonbonded interaction distances. Nonbonded interactions: 281407 Sorted by model distance: nonbonded pdb=" CG2 VAL A 190 " pdb=" O5' C b 400 " model vdw 0.984 3.460 nonbonded pdb=" CE MET B 337 " pdb=" CZ ARG L 78 " model vdw 1.076 3.690 nonbonded pdb=" CG2 VAL A 190 " pdb=" P C b 400 " model vdw 1.162 3.820 nonbonded pdb=" O THR G 236 " pdb=" NH1 ARG H 27 " model vdw 1.208 3.120 nonbonded pdb=" O THR F 236 " pdb=" NH1 ARG G 27 " model vdw 1.209 3.120 ... (remaining 281402 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } pdb_interpretation.ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 5.350 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: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.050 Process input model: 34.240 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 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 : 0.007 0.381 33890 Z= 0.368 Angle : 0.696 7.243 46104 Z= 0.396 Chirality : 0.053 0.271 5436 Planarity : 0.005 0.051 5580 Dihedral : 16.562 87.665 13308 Min Nonbonded Distance : 0.984 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.13), residues: 4020 helix: 0.73 (0.10), residues: 2784 sheet: -1.17 (0.32), residues: 180 loop : -0.41 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.032 0.003 TYR G 53 PHE 0.014 0.002 PHE K 169 TRP 0.005 0.001 TRP E 123 HIS 0.004 0.001 HIS L 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.29 (33888) covalent geometry : angle 0.69606 / 0.40 (46104) hydrogen bonds : bond 0.11155 / 7.63 ( 1969) hydrogen bonds : angle 5.77744 / 4.14 ( 5799) Misc. bond : bond 0.29988 / 15.51 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.4412 (mtm) cc_final: 0.3658 (mtp) REVERT: A 247 ILE cc_start: 0.8340 (mt) cc_final: 0.8125 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0752 time to fit residues: 4.5307 Evaluate side-chains 21 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.092 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0020 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.0464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 HIS ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.080720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066628 restraints weight = 11256.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068651 restraints weight = 7563.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.070240 restraints weight = 5549.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.071156 restraints weight = 4329.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.071927 restraints weight = 3618.979| |-----------------------------------------------------------------------------| r_work (final): 0.3289 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.062315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.060306 restraints weight = 1105.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061175 restraints weight = 346.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061600 restraints weight = 147.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061853 restraints weight = 70.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061975 restraints weight = 36.143| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.333 33890 Z= 0.270 Angle : 0.644 7.911 46104 Z= 0.311 Chirality : 0.046 0.299 5436 Planarity : 0.006 0.086 5580 Dihedral : 14.051 105.784 5760 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.13), residues: 4020 helix: 1.38 (0.10), residues: 2844 sheet: -1.43 (0.31), residues: 180 loop : -0.75 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 78 TYR 0.015 0.002 TYR A 252 PHE 0.011 0.002 PHE I 169 TRP 0.006 0.001 TRP B 261 HIS 0.002 0.001 HIS J 15 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (33888) covalent geometry : angle 0.64410 / 0.31 (46104) hydrogen bonds : bond 0.04233 / 2.82 ( 1969) hydrogen bonds : angle 4.28486 / 3.07 ( 5799) Misc. bond : bond 0.29437 / 14.98 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8557 (m-10) cc_final: 0.7644 (t80) REVERT: F 48 CYS cc_start: 0.9436 (m) cc_final: 0.9232 (m) REVERT: F 51 ILE cc_start: 0.8659 (mt) cc_final: 0.8398 (mt) REVERT: F 90 VAL cc_start: 0.8827 (m) cc_final: 0.8458 (t) REVERT: F 170 THR cc_start: 0.9129 (p) cc_final: 0.8802 (t) REVERT: F 303 HIS cc_start: 0.8343 (m90) cc_final: 0.7813 (m-70) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0737 time to fit residues: 10.0273 Evaluate side-chains 67 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.127 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0031 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 211 optimal weight: 0.0270 chunk 63 optimal weight: 0.6980 chunk 269 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 255 optimal weight: 0.9980 chunk 144 optimal weight: 0.0970 chunk 137 optimal weight: 0.0770 chunk 206 optimal weight: 0.2980 chunk 220 optimal weight: 0.9980 chunk 241 optimal weight: 0.9980 chunk 357 optimal weight: 1.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 15 HIS ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 HIS ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.081634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.067045 restraints weight = 11983.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.068896 restraints weight = 8121.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.070228 restraints weight = 6047.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.071185 restraints weight = 4835.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.071974 restraints weight = 4078.841| |-----------------------------------------------------------------------------| r_work (final): 0.3256 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.075247 restraints weight = 1355.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075831 restraints weight = 498.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076181 restraints weight = 233.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.076319 restraints weight = 106.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076419 restraints weight = 55.307| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.5574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.504 33890 Z= 1.194 Angle : 1.012 29.351 46104 Z= 0.540 Chirality : 0.055 0.428 5436 Planarity : 0.009 0.105 5580 Dihedral : 13.746 122.792 5760 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.13), residues: 4020 helix: 0.95 (0.10), residues: 2772 sheet: -1.84 (0.27), residues: 228 loop : -1.06 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 78 TYR 0.018 0.002 TYR B 23 PHE 0.010 0.001 PHE E 244 TRP 0.005 0.001 TRP L 261 HIS 0.004 0.001 HIS J 275 Details of bonding type rmsd/Z covalent geometry : bond 0.02239 / 1.17 (33888) covalent geometry : angle 1.01193 / 0.54 (46104) hydrogen bonds : bond 0.04340 / 2.91 ( 1969) hydrogen bonds : angle 4.38182 / 3.12 ( 5799) Misc. bond : bond 0.31088 / 15.86 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8636 (m-10) cc_final: 0.7602 (t80) REVERT: F 14 LYS cc_start: 0.8837 (mttt) cc_final: 0.8400 (mmtt) REVERT: F 145 ASN cc_start: 0.8177 (m110) cc_final: 0.7933 (m110) REVERT: F 225 ILE cc_start: 0.9231 (mt) cc_final: 0.8833 (mt) REVERT: F 239 LYS cc_start: 0.8244 (mttm) cc_final: 0.7958 (tptt) REVERT: F 272 MET cc_start: 0.7697 (mpp) cc_final: 0.7343 (mpp) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0697 time to fit residues: 7.4909 Evaluate side-chains 54 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.102 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 335 optimal weight: 0.9980 chunk 274 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 393 optimal weight: 7.9990 chunk 357 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 275 HIS F 303 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.078747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.065886 restraints weight = 12324.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.067783 restraints weight = 8212.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069162 restraints weight = 6007.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.070146 restraints weight = 4678.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070910 restraints weight = 3846.181| |-----------------------------------------------------------------------------| r_work (final): 0.3260 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.059000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058086 restraints weight = 1240.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058678 restraints weight = 354.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058868 restraints weight = 121.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058928 restraints weight = 44.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.058952 restraints weight = 18.092| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.6727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.517 33890 Z= 1.200 Angle : 0.990 28.975 46104 Z= 0.533 Chirality : 0.054 0.482 5436 Planarity : 0.007 0.079 5580 Dihedral : 13.861 131.443 5760 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.35 % Allowed : 3.14 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 4020 helix: 0.70 (0.10), residues: 2796 sheet: -2.04 (0.27), residues: 228 loop : -0.22 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.002 ARG K 339 TYR 0.032 0.003 TYR E 23 PHE 0.014 0.002 PHE B 248 TRP 0.010 0.002 TRP J 261 HIS 0.006 0.002 HIS I 15 Details of bonding type rmsd/Z covalent geometry : bond 0.02251 / 1.18 (33888) covalent geometry : angle 0.98969 / 0.53 (46104) hydrogen bonds : bond 0.04205 / 2.77 ( 1969) hydrogen bonds : angle 4.62078 / 3.33 ( 5799) Misc. bond : bond 0.31405 / 16.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 84 ARG cc_start: 0.9229 (ttp80) cc_final: 0.9019 (tpp-160) REVERT: F 193 ASP cc_start: 0.9295 (p0) cc_final: 0.8986 (p0) REVERT: F 231 LEU cc_start: 0.8777 (tp) cc_final: 0.8570 (tp) REVERT: F 239 LYS cc_start: 0.8345 (mttm) cc_final: 0.7880 (tptt) REVERT: F 305 ARG cc_start: 0.7037 (ptp-170) cc_final: 0.6660 (tmt-80) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.0567 time to fit residues: 4.7212 Evaluate side-chains 47 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.096 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0024 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 256 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 386 optimal weight: 0.6980 chunk 120 optimal weight: 0.0970 chunk 302 optimal weight: 5.9990 chunk 23 optimal weight: 0.0060 chunk 263 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 148 GLN F 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.080922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067641 restraints weight = 11681.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069685 restraints weight = 7725.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.071160 restraints weight = 5606.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.072250 restraints weight = 4373.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.072962 restraints weight = 3580.727| |-----------------------------------------------------------------------------| r_work (final): 0.3290 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.079960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077276 restraints weight = 1502.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.078626 restraints weight = 907.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.079273 restraints weight = 493.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079520 restraints weight = 198.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.079643 restraints weight = 112.332| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.511 33890 Z= 1.186 Angle : 0.936 29.195 46104 Z= 0.505 Chirality : 0.051 0.454 5436 Planarity : 0.005 0.035 5580 Dihedral : 13.577 128.128 5760 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.35 % Allowed : 4.53 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4020 helix: 0.78 (0.10), residues: 2844 sheet: -2.01 (0.28), residues: 228 loop : -0.68 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 151 TYR 0.022 0.002 TYR K 23 PHE 0.009 0.001 PHE D 244 TRP 0.006 0.001 TRP D 261 HIS 0.005 0.001 HIS J 303 Details of bonding type rmsd/Z covalent geometry : bond 0.02221 / 1.16 (33888) covalent geometry : angle 0.93635 / 0.51 (46104) hydrogen bonds : bond 0.03791 / 2.50 ( 1969) hydrogen bonds : angle 4.41825 / 3.16 ( 5799) Misc. bond : bond 0.29055 / 14.87 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 70 ILE cc_start: 0.9024 (mm) cc_final: 0.8816 (mm) REVERT: F 84 ARG cc_start: 0.9312 (ttp80) cc_final: 0.9063 (tpp-160) REVERT: F 171 LYS cc_start: 0.8579 (mmpt) cc_final: 0.8126 (mmmt) REVERT: F 193 ASP cc_start: 0.9311 (p0) cc_final: 0.9021 (p0) REVERT: F 239 LYS cc_start: 0.8302 (mttm) cc_final: 0.7871 (tptt) REVERT: F 290 ASP cc_start: 0.9052 (m-30) cc_final: 0.8849 (m-30) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.0786 time to fit residues: 6.4957 Evaluate side-chains 50 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.105 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 0.0020 chunk 96 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 206 optimal weight: 0.0060 chunk 381 optimal weight: 0.5980 chunk 375 optimal weight: 0.0970 chunk 369 optimal weight: 0.0470 chunk 106 optimal weight: 0.0570 chunk 159 optimal weight: 0.6980 overall best weight: 0.0418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 148 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.080975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.068382 restraints weight = 11597.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.070288 restraints weight = 7799.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.071681 restraints weight = 5703.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.072582 restraints weight = 4439.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.073486 restraints weight = 3675.712| |-----------------------------------------------------------------------------| r_work (final): 0.3313 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.063948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061841 restraints weight = 1179.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062781 restraints weight = 385.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.063345 restraints weight = 161.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063596 restraints weight = 76.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063745 restraints weight = 39.869| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.7478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.511 33890 Z= 1.185 Angle : 0.960 29.264 46104 Z= 0.514 Chirality : 0.051 0.466 5436 Planarity : 0.006 0.081 5580 Dihedral : 13.501 127.748 5760 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.13), residues: 4020 helix: 0.74 (0.10), residues: 2844 sheet: -2.26 (0.28), residues: 228 loop : -0.23 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 339 TYR 0.021 0.002 TYR J 23 PHE 0.010 0.001 PHE F 244 TRP 0.014 0.002 TRP F 261 HIS 0.003 0.001 HIS C 303 Details of bonding type rmsd/Z covalent geometry : bond 0.02219 / 1.16 (33888) covalent geometry : angle 0.96017 / 0.51 (46104) hydrogen bonds : bond 0.03822 / 2.54 ( 1969) hydrogen bonds : angle 4.42517 / 3.15 ( 5799) Misc. bond : bond 0.28804 / 14.74 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 70 ILE cc_start: 0.9038 (mm) cc_final: 0.8836 (mm) REVERT: F 84 ARG cc_start: 0.9290 (ttp80) cc_final: 0.9011 (tpm170) REVERT: F 171 LYS cc_start: 0.8388 (mmpt) cc_final: 0.7958 (mmmt) REVERT: F 193 ASP cc_start: 0.9305 (p0) cc_final: 0.9010 (p0) REVERT: F 203 ILE cc_start: 0.9383 (mm) cc_final: 0.9114 (pt) REVERT: F 231 LEU cc_start: 0.8795 (tp) cc_final: 0.8503 (tp) REVERT: F 239 LYS cc_start: 0.8208 (mttm) cc_final: 0.7836 (tptt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0713 time to fit residues: 5.6797 Evaluate side-chains 52 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.101 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 17 optimal weight: 30.0000 chunk 381 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 356 optimal weight: 0.8980 chunk 81 optimal weight: 0.0970 chunk 151 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 167 optimal weight: 0.4980 chunk 290 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067602 restraints weight = 11798.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069547 restraints weight = 8025.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.070936 restraints weight = 5900.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071901 restraints weight = 4613.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.072767 restraints weight = 3808.969| |-----------------------------------------------------------------------------| r_work (final): 0.3298 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.080749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.078690 restraints weight = 1450.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079719 restraints weight = 550.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.080129 restraints weight = 240.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.080350 restraints weight = 123.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.080473 restraints weight = 68.748| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.7755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.515 33890 Z= 1.185 Angle : 0.919 29.361 46104 Z= 0.505 Chirality : 0.050 0.378 5436 Planarity : 0.005 0.050 5580 Dihedral : 13.355 128.314 5760 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.14), residues: 4020 helix: 0.79 (0.10), residues: 2820 sheet: -2.23 (0.28), residues: 228 loop : -0.30 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 339 TYR 0.020 0.002 TYR J 23 PHE 0.009 0.001 PHE L 244 TRP 0.007 0.001 TRP B 261 HIS 0.003 0.001 HIS J 220 Details of bonding type rmsd/Z covalent geometry : bond 0.02218 / 1.16 (33888) covalent geometry : angle 0.91863 / 0.51 (46104) hydrogen bonds : bond 0.03593 / 2.39 ( 1969) hydrogen bonds : angle 4.57110 / 3.25 ( 5799) Misc. bond : bond 0.28797 / 14.72 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 10 ASP cc_start: 0.7202 (p0) cc_final: 0.6775 (p0) REVERT: F 14 LYS cc_start: 0.9114 (mttt) cc_final: 0.8758 (mttt) REVERT: F 84 ARG cc_start: 0.9321 (ttp80) cc_final: 0.9020 (tpm170) REVERT: F 171 LYS cc_start: 0.8038 (mmpt) cc_final: 0.7495 (mmmt) REVERT: F 193 ASP cc_start: 0.9329 (p0) cc_final: 0.9011 (p0) REVERT: F 231 LEU cc_start: 0.8788 (tp) cc_final: 0.8535 (tp) REVERT: F 239 LYS cc_start: 0.8205 (mttm) cc_final: 0.7725 (tptt) REVERT: F 272 MET cc_start: 0.7659 (mpp) cc_final: 0.6302 (mmm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0619 time to fit residues: 4.9419 Evaluate side-chains 46 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.110 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0028 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 66 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 204 optimal weight: 0.0570 chunk 102 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 395 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 324 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 377 optimal weight: 4.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 15 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.067562 restraints weight = 12012.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.069531 restraints weight = 8246.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.070958 restraints weight = 6051.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072066 restraints weight = 4749.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072877 restraints weight = 3854.709| |-----------------------------------------------------------------------------| r_work (final): 0.3298 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.075553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.074929 restraints weight = 1312.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.075299 restraints weight = 349.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.075453 restraints weight = 108.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.075496 restraints weight = 37.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.075520 restraints weight = 23.967| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.8032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.512 33890 Z= 1.185 Angle : 0.960 29.275 46104 Z= 0.513 Chirality : 0.050 0.443 5436 Planarity : 0.005 0.047 5580 Dihedral : 13.316 129.154 5760 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 23.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 4020 helix: 0.79 (0.10), residues: 2820 sheet: -2.17 (0.28), residues: 228 loop : -0.21 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 339 TYR 0.019 0.002 TYR I 23 PHE 0.013 0.001 PHE I 244 TRP 0.032 0.003 TRP C 261 HIS 0.003 0.001 HIS G 220 Details of bonding type rmsd/Z covalent geometry : bond 0.02219 / 1.16 (33888) covalent geometry : angle 0.96029 / 0.51 (46104) hydrogen bonds : bond 0.03451 / 2.28 ( 1969) hydrogen bonds : angle 4.50022 / 3.20 ( 5799) Misc. bond : bond 0.28741 / 14.70 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: F 10 ASP cc_start: 0.7461 (p0) cc_final: 0.7028 (p0) REVERT: F 14 LYS cc_start: 0.9064 (mttt) cc_final: 0.8552 (mttt) REVERT: F 23 TYR cc_start: 0.4028 (m-10) cc_final: 0.3780 (p90) REVERT: F 84 ARG cc_start: 0.9263 (ttp80) cc_final: 0.9014 (tpm170) REVERT: F 161 LEU cc_start: 0.9383 (mt) cc_final: 0.8721 (mt) REVERT: F 193 ASP cc_start: 0.9282 (p0) cc_final: 0.8932 (p0) REVERT: F 231 LEU cc_start: 0.8802 (tp) cc_final: 0.8555 (tp) REVERT: F 239 LYS cc_start: 0.8096 (mttm) cc_final: 0.7636 (tptt) REVERT: F 272 MET cc_start: 0.7740 (mpp) cc_final: 0.7444 (mmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0598 time to fit residues: 4.7007 Evaluate side-chains 47 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.109 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 0.0040 chunk 97 optimal weight: 0.3980 chunk 293 optimal weight: 0.0670 chunk 114 optimal weight: 0.0010 chunk 350 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 15 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068854 restraints weight = 11943.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.070903 restraints weight = 8065.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.072412 restraints weight = 5859.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.073528 restraints weight = 4537.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074393 restraints weight = 3659.577| |-----------------------------------------------------------------------------| r_work (final): 0.3344 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.065705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.062016 restraints weight = 1093.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.063342 restraints weight = 470.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064160 restraints weight = 256.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.064886 restraints weight = 154.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.065060 restraints weight = 80.104| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.8350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.512 33890 Z= 1.187 Angle : 0.973 29.311 46104 Z= 0.527 Chirality : 0.051 0.404 5436 Planarity : 0.005 0.048 5580 Dihedral : 13.260 129.676 5760 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.14), residues: 4020 helix: 0.70 (0.10), residues: 2832 sheet: -2.14 (0.30), residues: 228 loop : -0.08 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 339 TYR 0.019 0.002 TYR F 23 PHE 0.015 0.001 PHE B 244 TRP 0.027 0.003 TRP C 261 HIS 0.005 0.002 HIS G 220 Details of bonding type rmsd/Z covalent geometry : bond 0.02225 / 1.17 (33888) covalent geometry : angle 0.97338 / 0.53 (46104) hydrogen bonds : bond 0.03723 / 2.44 ( 1969) hydrogen bonds : angle 4.60516 / 3.28 ( 5799) Misc. bond : bond 0.28771 / 14.71 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: F 84 ARG cc_start: 0.9255 (ttp80) cc_final: 0.9041 (tpm170) REVERT: F 193 ASP cc_start: 0.9305 (p0) cc_final: 0.8973 (p0) REVERT: F 239 LYS cc_start: 0.8077 (mttm) cc_final: 0.7608 (tptt) REVERT: F 261 TRP cc_start: 0.7322 (m-10) cc_final: 0.6975 (m-10) REVERT: F 272 MET cc_start: 0.7758 (mpp) cc_final: 0.6695 (mtm) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0532 time to fit residues: 4.1032 Evaluate side-chains 46 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.103 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 30 optimal weight: 4.9990 chunk 365 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 17 optimal weight: 30.0000 chunk 343 optimal weight: 0.0170 chunk 277 optimal weight: 0.9980 chunk 2 optimal weight: 0.0370 chunk 383 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 390 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.082179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068731 restraints weight = 11776.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070705 restraints weight = 7967.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.072188 restraints weight = 5872.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073290 restraints weight = 4576.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.074157 restraints weight = 3733.629| |-----------------------------------------------------------------------------| r_work (final): 0.3346 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.076613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.075973 restraints weight = 1234.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.076319 restraints weight = 302.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.076460 restraints weight = 92.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.076490 restraints weight = 32.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.076492 restraints weight = 14.367| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.8643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.511 33890 Z= 1.200 Angle : 0.994 29.322 46104 Z= 0.536 Chirality : 0.050 0.399 5436 Planarity : 0.005 0.042 5580 Dihedral : 13.270 130.013 5760 Min Nonbonded Distance : 1.654 Molprobity Statistics. All-atom Clashscore : 25.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 4020 helix: 0.89 (0.10), residues: 2820 sheet: -2.17 (0.31), residues: 228 loop : -0.18 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 339 TYR 0.068 0.003 TYR A 23 PHE 0.014 0.001 PHE I 244 TRP 0.030 0.003 TRP C 261 HIS 0.009 0.002 HIS H 15 Details of bonding type rmsd/Z covalent geometry : bond 0.02221 / 1.16 (33888) covalent geometry : angle 0.99402 / 0.54 (46104) hydrogen bonds : bond 0.03765 / 2.47 ( 1969) hydrogen bonds : angle 4.66121 / 3.33 ( 5799) Misc. bond : bond 0.37745 / 19.55 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: F 84 ARG cc_start: 0.9239 (ttp80) cc_final: 0.9015 (tpm170) REVERT: F 193 ASP cc_start: 0.9320 (p0) cc_final: 0.8988 (p0) REVERT: F 231 LEU cc_start: 0.8726 (tp) cc_final: 0.8328 (tp) REVERT: F 239 LYS cc_start: 0.8076 (mttm) cc_final: 0.7503 (tptt) REVERT: F 272 MET cc_start: 0.7782 (mpp) cc_final: 0.6825 (mtm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0547 time to fit residues: 4.1208 Evaluate side-chains 48 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.100 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0025 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 208 optimal weight: 2.9990 chunk 18 optimal weight: 0.0980 chunk 112 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 295 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 338 optimal weight: 0.0970 chunk 157 optimal weight: 0.0040 chunk 302 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 368 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.081877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.068476 restraints weight = 11792.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.070342 restraints weight = 8052.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.071944 restraints weight = 6062.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.072900 restraints weight = 4710.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.073899 restraints weight = 3896.367| |-----------------------------------------------------------------------------| r_work (final): 0.3335 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.080514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077845 restraints weight = 1274.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079046 restraints weight = 591.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.079646 restraints weight = 298.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.080072 restraints weight = 158.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.080279 restraints weight = 81.476| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.8802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.514 33890 Z= 1.205 Angle : 0.981 29.742 46104 Z= 0.525 Chirality : 0.049 0.368 5436 Planarity : 0.008 0.101 5580 Dihedral : 13.285 128.683 5760 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 4020 helix: 0.92 (0.10), residues: 2820 sheet: -2.18 (0.31), residues: 228 loop : -0.24 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.002 ARG A 339 TYR 0.079 0.004 TYR G 23 PHE 0.012 0.001 PHE I 244 TRP 0.034 0.004 TRP K 261 HIS 0.006 0.001 HIS K 15 Details of bonding type rmsd/Z covalent geometry : bond 0.02236 / 1.17 (33888) covalent geometry : angle 0.98122 / 0.53 (46104) hydrogen bonds : bond 0.03539 / 2.32 ( 1969) hydrogen bonds : angle 4.56376 / 3.26 ( 5799) Misc. bond : bond 0.37224 / 19.26 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.81 seconds wall clock time: 45 minutes 43.71 seconds (2743.71 seconds total)