Starting phenix.real_space_refine on Tue Aug 26 03:14:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdn_17615/08_2025/8pdn_17615.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdn_17615/08_2025/8pdn_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 { model { file = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2025/8pdn_17615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2025/8pdn_17615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2025/8pdn_17615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdn_17615/08_2025/8pdn_17615.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 6.68, 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: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 4.05 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: 7.35 Time building geometry restraints manager: 3.90 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: 43917 1.45 - 2.90: 1988 2.90 - 4.35: 175 4.35 - 5.79: 0 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: 18479 17.53 - 35.07: 1861 35.07 - 52.60: 276 52.60 - 70.13: 120 70.13 - 87.67: 132 Dihedral angle restraints: 20868 sinusoidal: 9084 harmonic: 11784 Sorted by residual: dihedral pdb=" CA TYR F 59 " pdb=" C TYR F 59 " pdb=" N LYS F 60 " pdb=" CA LYS F 60 " ideal model delta harmonic sigma weight residual 180.00 -163.32 -16.68 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TYR L 59 " pdb=" C TYR L 59 " pdb=" N LYS L 60 " pdb=" CA LYS L 60 " ideal model delta harmonic sigma weight residual -180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA TYR B 59 " pdb=" C TYR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta harmonic sigma weight residual -180.00 -163.36 -16.64 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 20865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3456 0.036 - 0.072: 1463 0.072 - 0.108: 350 0.108 - 0.144: 138 0.144 - 0.180: 29 Chirality restraints: 5436 Sorted by residual: chirality pdb=" CB VAL K 35 " pdb=" CA VAL K 35 " pdb=" CG1 VAL K 35 " pdb=" CG2 VAL K 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CB VAL I 35 " pdb=" CA VAL I 35 " pdb=" CG1 VAL I 35 " pdb=" CG2 VAL I 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CB VAL B 35 " pdb=" CA VAL B 35 " pdb=" CG1 VAL B 35 " pdb=" CG2 VAL B 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.66e-01 ... (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: 0.12 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: 5.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 31.670 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:1.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 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 : 0.662 7.243 46104 Z= 0.394 Chirality : 0.044 0.180 5436 Planarity : 0.005 0.051 5580 Dihedral : 15.878 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 aren 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 covalent geometry : bond 0.00672 (33888) covalent geometry : angle 0.66180 (46104) hydrogen bonds : bond 0.11155 ( 1969) hydrogen bonds : angle 5.77744 ( 5799) Misc. bond : bond 0.29988 ( 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 : 0.078 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: 0.0663 time to fit residues: 3.9842 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 : 0.069 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: 0.0016 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... Flipped N/Q/H residues before XYZ refinement: F 15 HIS ** F 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.066767 restraints weight = 11172.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.068865 restraints weight = 7310.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.070456 restraints weight = 5234.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.071628 restraints weight = 4018.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.072299 restraints weight = 3245.602| |-----------------------------------------------------------------------------| r_work (final): 0.3299 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068737 restraints weight = 1496.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.069406 restraints weight = 330.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069687 restraints weight = 131.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069804 restraints weight = 49.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069872 restraints weight = 23.532| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.338 33890 Z= 0.267 Angle : 0.570 5.952 46104 Z= 0.306 Chirality : 0.039 0.125 5436 Planarity : 0.006 0.089 5580 Dihedral : 12.309 73.856 5760 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.35 % Allowed : 2.09 % 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 aren not related in a simple way. whole: 1.01 (0.13), residues: 4020 helix: 1.34 (0.10), residues: 2844 sheet: -1.46 (0.31), residues: 180 loop : -0.72 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 78 TYR 0.017 0.002 TYR E 252 PHE 0.013 0.002 PHE I 169 TRP 0.006 0.001 TRP D 261 HIS 0.003 0.001 HIS L 15 Details of bonding type rmsd covalent geometry : bond 0.00279 (33888) covalent geometry : angle 0.56983 (46104) hydrogen bonds : bond 0.04063 ( 1969) hydrogen bonds : angle 4.24674 ( 5799) Misc. bond : bond 0.29685 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8576 (m-10) cc_final: 0.7629 (t80) REVERT: F 51 ILE cc_start: 0.8692 (mt) cc_final: 0.8379 (mt) REVERT: F 90 VAL cc_start: 0.8673 (m) cc_final: 0.8439 (t) REVERT: F 170 THR cc_start: 0.9095 (p) cc_final: 0.8793 (t) REVERT: F 303 HIS cc_start: 0.8439 (m90) cc_final: 0.7875 (m-70) outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.0763 time to fit residues: 10.4783 Evaluate side-chains 68 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.106 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 : 0.001 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.080634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.066274 restraints weight = 12232.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068265 restraints weight = 8061.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.069648 restraints weight = 5900.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.070710 restraints weight = 4661.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071436 restraints weight = 3878.987| |-----------------------------------------------------------------------------| r_work (final): 0.3253 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.066157 restraints weight = 1801.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.067093 restraints weight = 809.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.067464 restraints weight = 324.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.067617 restraints weight = 157.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067684 restraints weight = 84.781| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.480 33890 Z= 0.367 Angle : 0.852 12.568 46104 Z= 0.434 Chirality : 0.046 0.196 5436 Planarity : 0.007 0.077 5580 Dihedral : 12.254 74.615 5760 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 aren not related in a simple way. whole: 0.27 (0.13), residues: 4020 helix: 0.90 (0.10), residues: 2844 sheet: -2.32 (0.25), residues: 228 loop : -1.18 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 339 TYR 0.052 0.003 TYR G 23 PHE 0.011 0.001 PHE D 244 TRP 0.007 0.002 TRP E 261 HIS 0.015 0.003 HIS D 15 Details of bonding type rmsd covalent geometry : bond 0.00510 (33888) covalent geometry : angle 0.85236 (46104) hydrogen bonds : bond 0.04201 ( 1969) hydrogen bonds : angle 4.39598 ( 5799) Misc. bond : bond 0.38364 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: F 13 TYR cc_start: 0.8525 (m-10) cc_final: 0.7567 (t80) REVERT: F 80 GLN cc_start: 0.8615 (tt0) cc_final: 0.8391 (tm-30) REVERT: F 145 ASN cc_start: 0.8176 (m110) cc_final: 0.7957 (m110) REVERT: F 149 ASN cc_start: 0.8105 (p0) cc_final: 0.7857 (p0) REVERT: F 239 LYS cc_start: 0.8258 (mttm) cc_final: 0.7917 (tptt) REVERT: F 272 MET cc_start: 0.7756 (mpp) cc_final: 0.7235 (mpp) REVERT: F 303 HIS cc_start: 0.8336 (m90) cc_final: 0.7598 (m-70) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.0750 time to fit residues: 8.0437 Evaluate side-chains 57 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.104 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 335 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 chunk 357 optimal weight: 0.0060 chunk 254 optimal weight: 6.9990 chunk 315 optimal weight: 0.9990 chunk 258 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 275 HIS F 344 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.068422 restraints weight = 11762.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.070545 restraints weight = 7676.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.072048 restraints weight = 5510.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.073101 restraints weight = 4258.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073809 restraints weight = 3490.764| |-----------------------------------------------------------------------------| r_work (final): 0.3315 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.068004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.066413 restraints weight = 1742.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.067174 restraints weight = 704.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.067559 restraints weight = 333.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.067779 restraints weight = 162.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.067887 restraints weight = 83.330| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.434 33890 Z= 0.322 Angle : 0.718 7.982 46104 Z= 0.377 Chirality : 0.043 0.146 5436 Planarity : 0.006 0.068 5580 Dihedral : 12.326 74.192 5760 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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 aren not related in a simple way. whole: -0.10 (0.13), residues: 4020 helix: 0.58 (0.09), residues: 2832 sheet: -2.18 (0.27), residues: 228 loop : -1.18 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 305 TYR 0.028 0.003 TYR K 23 PHE 0.007 0.001 PHE I 169 TRP 0.024 0.003 TRP H 261 HIS 0.004 0.001 HIS G 15 Details of bonding type rmsd covalent geometry : bond 0.00401 (33888) covalent geometry : angle 0.71783 (46104) hydrogen bonds : bond 0.03884 ( 1969) hydrogen bonds : angle 4.37165 ( 5799) Misc. bond : bond 0.35004 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.083 Fit side-chains revert: symmetry clash REVERT: F 80 GLN cc_start: 0.8606 (tt0) cc_final: 0.8370 (tm-30) REVERT: F 145 ASN cc_start: 0.8175 (m110) cc_final: 0.7942 (m110) REVERT: F 239 LYS cc_start: 0.8251 (mttm) cc_final: 0.7908 (tptt) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0663 time to fit residues: 5.9980 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 : 0.106 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: 0.0016 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: 5.9990 chunk 113 optimal weight: 7.9990 chunk 386 optimal weight: 0.0070 chunk 120 optimal weight: 1.9990 chunk 302 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 263 optimal weight: 0.0470 chunk 341 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 overall best weight: 2.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.079811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.067052 restraints weight = 11439.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.069031 restraints weight = 7524.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.070418 restraints weight = 5433.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.071420 restraints weight = 4204.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072218 restraints weight = 3441.127| |-----------------------------------------------------------------------------| r_work (final): 0.3287 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.069264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.068645 restraints weight = 1750.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068961 restraints weight = 433.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.069148 restraints weight = 157.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.069210 restraints weight = 59.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.069241 restraints weight = 25.663| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.476 33890 Z= 0.333 Angle : 0.688 6.698 46104 Z= 0.364 Chirality : 0.043 0.144 5436 Planarity : 0.006 0.067 5580 Dihedral : 12.430 73.347 5760 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.35 % Allowed : 4.18 % Favored : 95.47 % 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 aren not related in a simple way. whole: -0.13 (0.13), residues: 4020 helix: 0.50 (0.09), residues: 2832 sheet: -2.32 (0.27), residues: 228 loop : -0.94 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 78 TYR 0.072 0.003 TYR C 23 PHE 0.012 0.002 PHE B 224 TRP 0.012 0.002 TRP I 261 HIS 0.005 0.001 HIS I 15 Details of bonding type rmsd covalent geometry : bond 0.00381 (33888) covalent geometry : angle 0.68792 (46104) hydrogen bonds : bond 0.03812 ( 1969) hydrogen bonds : angle 4.49855 ( 5799) Misc. bond : bond 0.37563 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 70 ILE cc_start: 0.9099 (mm) cc_final: 0.8897 (mm) REVERT: F 80 GLN cc_start: 0.8492 (tt0) cc_final: 0.8235 (tm-30) REVERT: F 113 MET cc_start: 0.8549 (pmm) cc_final: 0.8346 (pmm) REVERT: F 149 ASN cc_start: 0.7896 (p0) cc_final: 0.7677 (p0) REVERT: F 239 LYS cc_start: 0.8295 (mttm) cc_final: 0.7947 (tptt) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.0409 time to fit residues: 3.2934 Evaluate side-chains 44 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.063 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: 0.0016 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: 0.6980 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 51 optimal weight: 0.0370 chunk 61 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 381 optimal weight: 0.0870 chunk 375 optimal weight: 9.9990 chunk 369 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 159 optimal weight: 9.9990 overall best weight: 0.9238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 GLN F 303 HIS F 306 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.081936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.069097 restraints weight = 11491.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.071256 restraints weight = 7403.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.072742 restraints weight = 5263.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.073905 restraints weight = 4021.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.074592 restraints weight = 3224.122| |-----------------------------------------------------------------------------| r_work (final): 0.3325 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.071227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.070184 restraints weight = 1870.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.070750 restraints weight = 567.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.071035 restraints weight = 235.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.071114 restraints weight = 93.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071160 restraints weight = 42.853| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.7393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.465 33890 Z= 0.317 Angle : 0.640 8.211 46104 Z= 0.342 Chirality : 0.042 0.139 5436 Planarity : 0.005 0.045 5580 Dihedral : 12.539 73.437 5760 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.05 % Allowed : 4.18 % 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 aren not related in a simple way. whole: -0.14 (0.13), residues: 4020 helix: 0.47 (0.10), residues: 2832 sheet: -2.19 (0.28), residues: 228 loop : -0.89 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 78 TYR 0.062 0.003 TYR L 23 PHE 0.021 0.002 PHE E 248 TRP 0.020 0.002 TRP G 261 HIS 0.005 0.001 HIS C 15 Details of bonding type rmsd covalent geometry : bond 0.00334 (33888) covalent geometry : angle 0.64012 (46104) hydrogen bonds : bond 0.03602 ( 1969) hydrogen bonds : angle 4.56379 ( 5799) Misc. bond : bond 0.36770 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 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: 3 poor density : 64 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: F 80 GLN cc_start: 0.8380 (tt0) cc_final: 0.8043 (tm-30) REVERT: F 149 ASN cc_start: 0.7927 (p0) cc_final: 0.7673 (p0) REVERT: F 239 LYS cc_start: 0.8178 (mttm) cc_final: 0.7774 (tptt) REVERT: F 247 ILE cc_start: 0.9520 (mm) cc_final: 0.9123 (tt) outliers start: 3 outliers final: 0 residues processed: 66 average time/residue: 0.0484 time to fit residues: 4.0102 Evaluate side-chains 43 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.074 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: 0.0016 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 ------------------------------------------------------------------------------- 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: 0.6980 chunk 381 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 151 optimal weight: 0.0020 chunk 22 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 290 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 216 optimal weight: 0.5980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.082439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.069531 restraints weight = 11461.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.071592 restraints weight = 7652.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073066 restraints weight = 5526.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074194 restraints weight = 4305.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074903 restraints weight = 3490.216| |-----------------------------------------------------------------------------| r_work (final): 0.3328 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.071032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.069899 restraints weight = 1569.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070445 restraints weight = 487.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070739 restraints weight = 213.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.070878 restraints weight = 100.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.070922 restraints weight = 54.116| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.441 33890 Z= 0.306 Angle : 0.646 6.319 46104 Z= 0.345 Chirality : 0.043 0.152 5436 Planarity : 0.005 0.053 5580 Dihedral : 12.662 73.414 5760 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.35 % Allowed : 2.79 % Favored : 96.86 % 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 aren not related in a simple way. whole: -0.19 (0.14), residues: 4020 helix: 0.38 (0.10), residues: 2832 sheet: -2.26 (0.29), residues: 228 loop : -0.73 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 78 TYR 0.061 0.003 TYR G 23 PHE 0.017 0.001 PHE G 248 TRP 0.013 0.002 TRP D 261 HIS 0.003 0.001 HIS H 303 Details of bonding type rmsd covalent geometry : bond 0.00319 (33888) covalent geometry : angle 0.64574 (46104) hydrogen bonds : bond 0.03704 ( 1969) hydrogen bonds : angle 4.67972 ( 5799) Misc. bond : bond 0.35450 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 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: 1 poor density : 61 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: F 70 ILE cc_start: 0.9035 (mm) cc_final: 0.8833 (mm) REVERT: F 80 GLN cc_start: 0.8402 (tt0) cc_final: 0.8036 (tm-30) REVERT: F 239 LYS cc_start: 0.8208 (mttm) cc_final: 0.7820 (tptt) REVERT: F 247 ILE cc_start: 0.9482 (mm) cc_final: 0.9069 (tt) REVERT: F 303 HIS cc_start: 0.8509 (m-70) cc_final: 0.8118 (m-70) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.0497 time to fit residues: 3.9547 Evaluate side-chains 42 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.115 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 66 optimal weight: 6.9990 chunk 105 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 204 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 395 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 143 optimal weight: 0.0770 chunk 377 optimal weight: 8.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.071844 restraints weight = 11840.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.073915 restraints weight = 7959.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.075398 restraints weight = 5815.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.076515 restraints weight = 4545.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.077189 restraints weight = 3721.557| |-----------------------------------------------------------------------------| r_work (final): 0.3359 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.069388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.067793 restraints weight = 1463.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.068384 restraints weight = 489.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.068757 restraints weight = 246.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.068962 restraints weight = 149.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.069159 restraints weight = 99.248| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.8224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.417 33890 Z= 0.294 Angle : 0.640 5.691 46104 Z= 0.341 Chirality : 0.042 0.156 5436 Planarity : 0.007 0.110 5580 Dihedral : 12.645 73.353 5760 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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 aren not related in a simple way. whole: -0.03 (0.14), residues: 4020 helix: 0.51 (0.10), residues: 2844 sheet: -2.24 (0.31), residues: 228 loop : -0.72 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 84 TYR 0.052 0.003 TYR G 23 PHE 0.016 0.002 PHE F 248 TRP 0.010 0.001 TRP F 261 HIS 0.002 0.001 HIS G 220 Details of bonding type rmsd covalent geometry : bond 0.00307 (33888) covalent geometry : angle 0.64007 (46104) hydrogen bonds : bond 0.03355 ( 1969) hydrogen bonds : angle 4.59459 ( 5799) Misc. bond : bond 0.33880 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.065 Fit side-chains REVERT: F 76 SER cc_start: 0.7648 (m) cc_final: 0.7031 (p) REVERT: F 80 GLN cc_start: 0.8294 (tt0) cc_final: 0.7971 (tm-30) REVERT: F 171 LYS cc_start: 0.8418 (mmpt) cc_final: 0.7930 (mmmt) REVERT: F 239 LYS cc_start: 0.7996 (mttm) cc_final: 0.7725 (tptt) REVERT: F 278 VAL cc_start: 0.9164 (t) cc_final: 0.8958 (t) REVERT: F 303 HIS cc_start: 0.8533 (m-70) cc_final: 0.8049 (m-70) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0496 time to fit residues: 3.9276 Evaluate side-chains 42 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.111 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: 6.9990 chunk 97 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 350 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 214 optimal weight: 2.9990 chunk 287 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.083411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.070693 restraints weight = 12086.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.072737 restraints weight = 8106.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.074209 restraints weight = 5878.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075270 restraints weight = 4548.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075843 restraints weight = 3700.071| |-----------------------------------------------------------------------------| r_work (final): 0.3328 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.068544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.066929 restraints weight = 1455.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.067583 restraints weight = 537.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.067939 restraints weight = 266.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.068154 restraints weight = 156.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.068194 restraints weight = 90.676| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.8556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.409 33890 Z= 0.302 Angle : 0.696 13.724 46104 Z= 0.363 Chirality : 0.044 0.148 5436 Planarity : 0.006 0.105 5580 Dihedral : 12.774 73.550 5760 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 aren not related in a simple way. whole: 0.04 (0.14), residues: 4020 helix: 0.57 (0.10), residues: 2844 sheet: -2.37 (0.31), residues: 228 loop : -0.67 (0.22), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 27 TYR 0.050 0.003 TYR G 23 PHE 0.015 0.001 PHE B 248 TRP 0.018 0.002 TRP J 261 HIS 0.003 0.001 HIS G 220 Details of bonding type rmsd covalent geometry : bond 0.00360 (33888) covalent geometry : angle 0.69622 (46104) hydrogen bonds : bond 0.03371 ( 1969) hydrogen bonds : angle 4.68403 ( 5799) Misc. bond : bond 0.33711 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 70 ILE cc_start: 0.8995 (mm) cc_final: 0.8780 (mm) REVERT: F 76 SER cc_start: 0.7639 (m) cc_final: 0.6962 (p) REVERT: F 80 GLN cc_start: 0.8464 (tt0) cc_final: 0.8087 (tm-30) REVERT: F 171 LYS cc_start: 0.8507 (mmpt) cc_final: 0.8019 (mmmt) REVERT: F 239 LYS cc_start: 0.8252 (mttm) cc_final: 0.7387 (tptt) REVERT: F 272 MET cc_start: 0.8314 (mtm) cc_final: 0.8073 (mtm) REVERT: F 303 HIS cc_start: 0.8542 (m-70) cc_final: 0.8131 (m-70) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0629 time to fit residues: 4.2243 Evaluate side-chains 42 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 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: 0.0024 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 30 optimal weight: 0.9990 chunk 365 optimal weight: 0.0870 chunk 120 optimal weight: 0.5980 chunk 17 optimal weight: 30.0000 chunk 343 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 383 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 15 HIS ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.083986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070892 restraints weight = 11876.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.072616 restraints weight = 8096.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.074158 restraints weight = 6143.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.075183 restraints weight = 4776.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.076009 restraints weight = 3920.029| |-----------------------------------------------------------------------------| r_work (final): 0.3343 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.066779 restraints weight = 1600.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.067441 restraints weight = 620.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067679 restraints weight = 296.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.067906 restraints weight = 173.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.067992 restraints weight = 74.128| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.8780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.404 33890 Z= 0.295 Angle : 0.759 19.908 46104 Z= 0.368 Chirality : 0.043 0.198 5436 Planarity : 0.006 0.100 5580 Dihedral : 12.642 73.551 5760 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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 aren not related in a simple way. whole: 0.03 (0.14), residues: 4020 helix: 0.59 (0.10), residues: 2832 sheet: -2.52 (0.31), residues: 228 loop : -0.70 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 84 TYR 0.047 0.003 TYR G 23 PHE 0.014 0.001 PHE G 248 TRP 0.024 0.003 TRP A 261 HIS 0.005 0.001 HIS F 15 Details of bonding type rmsd covalent geometry : bond 0.00338 (33888) covalent geometry : angle 0.75873 (46104) hydrogen bonds : bond 0.03529 ( 1969) hydrogen bonds : angle 4.73848 ( 5799) Misc. bond : bond 0.33276 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 80 GLN cc_start: 0.8333 (tt0) cc_final: 0.7958 (tm-30) REVERT: F 171 LYS cc_start: 0.8369 (mmpt) cc_final: 0.7859 (mmmt) REVERT: F 239 LYS cc_start: 0.7788 (mttm) cc_final: 0.7341 (tptt) REVERT: F 303 HIS cc_start: 0.8490 (m-70) cc_final: 0.8022 (m-70) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0609 time to fit residues: 4.4447 Evaluate side-chains 41 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 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: 0.0024 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 208 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 374 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 338 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 368 optimal weight: 0.0970 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070341 restraints weight = 11634.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.072265 restraints weight = 7960.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.073633 restraints weight = 5883.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.074709 restraints weight = 4637.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.075437 restraints weight = 3814.125| |-----------------------------------------------------------------------------| r_work (final): 0.3349 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.070480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.069036 restraints weight = 1491.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.069819 restraints weight = 481.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.070130 restraints weight = 195.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.070262 restraints weight = 97.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070370 restraints weight = 49.979| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.9062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.395 33890 Z= 0.287 Angle : 0.751 21.114 46104 Z= 0.367 Chirality : 0.044 0.220 5436 Planarity : 0.006 0.094 5580 Dihedral : 12.766 73.511 5760 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 aren not related in a simple way. whole: -0.13 (0.14), residues: 4020 helix: 0.49 (0.10), residues: 2820 sheet: -2.63 (0.30), residues: 228 loop : -0.80 (0.22), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 293 TYR 0.043 0.003 TYR F 23 PHE 0.016 0.001 PHE G 248 TRP 0.015 0.002 TRP J 261 HIS 0.015 0.002 HIS I 15 Details of bonding type rmsd covalent geometry : bond 0.00319 (33888) covalent geometry : angle 0.75109 (46104) hydrogen bonds : bond 0.03532 ( 1969) hydrogen bonds : angle 4.92459 ( 5799) Misc. bond : bond 0.32589 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.75 seconds wall clock time: 40 minutes 8.92 seconds (2408.92 seconds total)